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samples.\n",{"type":429,"tag":531,"props":677,"children":678},{},[679,689],{"type":429,"tag":495,"props":680,"children":681},{},[682,687],{"type":429,"tag":440,"props":683,"children":684},{},[685],{"type":444,"value":686},"Dense mode",{"type":444,"value":688},": a compact display showing density plots for SVs and SNV/indels",{"type":429,"tag":495,"props":690,"children":691},{},[692,697],{"type":429,"tag":440,"props":693,"children":694},{},[695],{"type":444,"value":696},"Expanded mode",{"type":444,"value":698},": all types of mutations are aligned by samples, one row per sample",{"type":429,"tag":495,"props":700,"children":701},{},[702,706],{"type":429,"tag":440,"props":703,"children":704},{},[705],{"type":444,"value":646},{"type":444,"value":707},": showing mutations for one sample alone, along with any available genomic assay tracks.",{"type":429,"tag":495,"props":709,"children":710},{},[711,715],{"type":429,"tag":440,"props":712,"children":713},{},[714],{"type":444,"value":653},{"type":444,"value":716},": combining the mutation profiles of multiple genomic regions in one view, in the form of a sample-by-region matrix.",{"type":429,"tag":453,"props":718,"children":720},{"id":719},"cohort-view",[721],{"type":444,"value":639},{"type":429,"tag":436,"props":723,"children":724},{},[725],{"type":444,"value":726},"Cohort View connects DNA alterations with gene expression across a cohort.\nIt shows in either \"dense\" or \"expanded\" mode.",{"type":429,"tag":464,"props":728,"children":730},{"id":729},"dense-mode",[731],{"type":444,"value":686},{"type":429,"tag":436,"props":733,"children":734},{},[735],{"type":444,"value":736},"By default, the \"Pediatric tumor mutation\" track displays the cohort-view compactly in \"dense\" mode.\nThis view is consisted of following parts:",{"type":429,"tag":531,"props":738,"children":739},{},[740,745,750,755,760],{"type":429,"tag":495,"props":741,"children":742},{},[743],{"type":444,"value":744},"SNV/indel and SV/fusion breakpoint density plots on top;",{"type":429,"tag":495,"props":746,"children":747},{},[748],{"type":444,"value":749},"Cancer group labels on left;",{"type":429,"tag":495,"props":751,"children":752},{},[753],{"type":444,"value":754},"CNV and LOH segment plots in the center;",{"type":429,"tag":495,"props":756,"children":757},{},[758],{"type":444,"value":759},"Gene expression ranking on right;",{"type":429,"tag":495,"props":761,"children":762},{},[763],{"type":444,"value":764},"Legends at bottom.",{"type":429,"tag":436,"props":766,"children":767},{},[768],{"type":429,"tag":514,"props":769,"children":772},{"alt":770,"src":771},"img 68","/img/visualization-community/genomepaint/genomepaint-user-guide/image68.png",[],{"type":429,"tag":774,"props":775,"children":777},"h4",{"id":776},"mutation-and-breakpoint-density-plot-in-dense-mode",[778],{"type":444,"value":779},"Mutation and breakpoint density plot in dense mode",{"type":429,"tag":436,"props":781,"children":782},{},[783],{"type":444,"value":784},"At the top, dots indicate the density of SV breakpoints and SNV/indels from every sample combined.\nDot size represents the number of samples.\nFor SNV/indel, dot colors represent mutation classes.\nFor SV, each dot represents one or more samples from the same cancer type.\nHover over a dot for details:",{"type":429,"tag":436,"props":786,"children":787},{},[788],{"type":429,"tag":514,"props":789,"children":792},{"alt":790,"src":791},"img 41","/img/visualization-community/genomepaint/genomepaint-user-guide/image41.png",[],{"type":429,"tag":436,"props":794,"children":795},{},[796],{"type":444,"value":797},"Above example shows KRAS gene locus at a low resolution and its exon as a thin sliver.\nAll missense mutations from that exon are represented by one big dot.\nZoom in on the exon and the large dot will break up to smaller dots.",{"type":429,"tag":436,"props":799,"children":800},{},[801],{"type":429,"tag":514,"props":802,"children":805},{"alt":803,"src":804},"img 20","/img/visualization-community/genomepaint/genomepaint-user-guide/image20.png",[],{"type":429,"tag":436,"props":807,"children":808},{},[809],{"type":444,"value":810},"Zooming in at base-pair level, each dot now represents the collection of all mutations at one base-pair; it's also positioned to that base-pair.",{"type":429,"tag":436,"props":812,"children":813},{},[814],{"type":429,"tag":514,"props":815,"children":818},{"alt":816,"src":817},"img 53","/img/visualization-community/genomepaint/genomepaint-user-guide/image53.png",[],{"type":429,"tag":436,"props":820,"children":821},{},[822],{"type":444,"value":823},"Clicking on a dot to show the actual list of mutations.\nFrom this panel, hover over a sample to see sample-level information about this mutation.",{"type":429,"tag":436,"props":825,"children":826},{},[827],{"type":429,"tag":514,"props":828,"children":831},{"alt":829,"src":830},"img 22","/img/visualization-community/genomepaint/genomepaint-user-guide/image22.png",[],{"type":429,"tag":774,"props":833,"children":835},{"id":834},"dbsnp-and-clinvar-matching",[836],{"type":444,"value":837},"dbSNP and ClinVar matching",{"type":429,"tag":436,"props":839,"children":840},{},[841],{"type":444,"value":842},"At the bottom of the mutation tooltip shows if any dbSNP or ClinVar entry matches with the mutation.",{"type":429,"tag":436,"props":844,"children":845},{},[846],{"type":429,"tag":514,"props":847,"children":850},{"alt":848,"src":849},"img 15","/img/visualization-community/genomepaint/genomepaint-user-guide/image15.png",[],{"type":429,"tag":436,"props":852,"children":853},{},[854],{"type":444,"value":855},"Either match will be shown as URL links to their respective databases.",{"type":429,"tag":436,"props":857,"children":858},{},[859],{"type":444,"value":860},"(You can't click the link in a mouse-hover tooltip; simply click on the mutation from GenomePaint to show the information panel with this information, there you will be able to click the dbSNP or ClinVar link.\nThe panel will only go away if you choose to hide it.)",{"type":429,"tag":436,"props":862,"children":863},{},[864],{"type":444,"value":865},"This matching is conducted on-the-fly using GenomePaint's backend databases, and is also available to a hg19 or hg38 custom GenomePaint track which does not need to pre-annotate its variants with the dbSNP or ClinVar.",{"type":429,"tag":774,"props":867,"children":869},{"id":868},"cnvloh-in-dense-mode",[870],{"type":444,"value":871},"CNV/LOH in dense mode",{"type":429,"tag":436,"props":873,"children":874},{},[875],{"type":444,"value":876},"In this part, GenomePaint shows CNV/LOH and expression rank aligned by rows, one row per sample.\nCNV and LOH events are shown as thin horizontal lines, identified by color:",{"type":429,"tag":531,"props":878,"children":879},{},[880,885,890],{"type":429,"tag":495,"props":881,"children":882},{},[883],{"type":444,"value":884},"Red: copy number gain",{"type":429,"tag":495,"props":886,"children":887},{},[888],{"type":444,"value":889},"Blue: copy number loss",{"type":429,"tag":495,"props":891,"children":892},{},[893],{"type":444,"value":894},"Gray: LOH",{"type":429,"tag":436,"props":896,"children":897},{},[898],{"type":444,"value":899},"In all cases, the color darkness represents the degree of the event, see color scales in legend.",{"type":429,"tag":436,"props":901,"children":902},{},[903],{"type":444,"value":904},"Samples are grouped by cancer type, as shown by the cancer type names on the left.\nEach cancer type is labeled by abbreviations.\nHover over the label for details.",{"type":429,"tag":436,"props":906,"children":907},{},[908],{"type":429,"tag":514,"props":909,"children":912},{"alt":910,"src":911},"img 33","/img/visualization-community/genomepaint/genomepaint-user-guide/image33.png",[],{"type":429,"tag":436,"props":914,"children":915},{},[916,918,924],{"type":444,"value":917},"You can filter mutation data by cancer type. See section ",{"type":429,"tag":476,"props":919,"children":921},{"href":920},"#cancer-type-filter",[922],{"type":444,"value":923},"Cancer type filter",{"type":444,"value":484},{"type":429,"tag":464,"props":926,"children":928},{"id":927},"expanded-mode",[929],{"type":444,"value":696},{"type":429,"tag":436,"props":931,"children":932},{},[933],{"type":444,"value":934},"On the top right, click \"CONFIG\" to show the configuration menu, then choose \"Expanded\" to go into expanded mode:",{"type":429,"tag":436,"props":936,"children":937},{},[938],{"type":429,"tag":514,"props":939,"children":942},{"alt":940,"src":941},"img 51","/img/visualization-community/genomepaint/genomepaint-user-guide/image51.png",[],{"type":429,"tag":436,"props":944,"children":945},{},[946],{"type":444,"value":947},"The expanded mode looks like below:",{"type":429,"tag":436,"props":949,"children":950},{},[951],{"type":429,"tag":514,"props":952,"children":955},{"alt":953,"src":954},"img 67","/img/visualization-community/genomepaint/genomepaint-user-guide/image67.png",[],{"type":429,"tag":436,"props":957,"children":958},{},[959],{"type":444,"value":960},"In expanded mode, all mutations for each sample are shown in the same row.\nCircles represent SV/fusion breakpoints, and x marks represent SNV/indels, all overlaying with CNV/LOH.\nSNV/indels and breakpoints are always shown on top of CNV and LOH.\nText labels can be shown for SV/fusion/SNV/indel, if available.",{"type":429,"tag":774,"props":962,"children":964},{"id":963},"cnv-display-and-configuration",[965],{"type":444,"value":966},"CNV display and configuration",{"type":429,"tag":436,"props":968,"children":969},{},[970],{"type":444,"value":971},"This section applies to both dense and expanded modes.",{"type":429,"tag":436,"props":973,"children":974},{},[975],{"type":444,"value":976},"CNVs are horizontal bars, with red for gain and blue for loss, and darkness by the log2(ratio).\nHover over a CNV for details:",{"type":429,"tag":436,"props":978,"children":979},{},[980],{"type":429,"tag":514,"props":981,"children":984},{"alt":982,"src":983},"img 39","/img/visualization-community/genomepaint/genomepaint-user-guide/image39.png",[],{"type":429,"tag":436,"props":986,"children":987},{},[988],{"type":444,"value":989},"The log2(ratio) color scale from CNVs in the view range is shown in the legend:",{"type":429,"tag":436,"props":991,"children":992},{},[993],{"type":429,"tag":514,"props":994,"children":997},{"alt":995,"src":996},"img 75","/img/visualization-community/genomepaint/genomepaint-user-guide/image75.png",[],{"type":429,"tag":436,"props":999,"children":1000},{},[1001],{"type":444,"value":1002},"To prevent outlier log2(ratio) value from skewing the view, the cutoff value is set by the upper whisker value of boxplot ( (3rd quartile) + 1.5 * (interquartile range), if smaller than the maximum value).",{"type":429,"tag":436,"props":1004,"children":1005},{},[1006],{"type":444,"value":1007},"A size limit may be used to show only focal events but not arm-level events.\nBy default, the size limit is 2 Mb, and CNV segments wider than 2 Mb will not be shown.\nClick the \"CONFIG\" label at the right of the track to change this cutoff.",{"type":429,"tag":436,"props":1009,"children":1010},{},[1011],{"type":429,"tag":514,"props":1012,"children":1015},{"alt":1013,"src":1014},"img 28","/img/visualization-community/genomepaint/genomepaint-user-guide/image28.png",[],{"type":429,"tag":436,"props":1017,"children":1018},{},[1019],{"type":444,"value":1020},"By setting the size limit to 0, the limit will be disabled and CNV of all sizes will be shown.",{"type":429,"tag":436,"props":1022,"children":1023},{},[1024],{"type":444,"value":1025},"Similarly, CNVs can be filtered by log2(ratio) value, where CNV with absolute log2(ratio) lower than the cutoff will not be shown.",{"type":429,"tag":436,"props":1027,"children":1028},{},[1029,1031,1036],{"type":444,"value":1030},"Click on a CNV segment to launch the Sample View, see the section on ",{"type":429,"tag":476,"props":1032,"children":1034},{"href":1033},"#sample-view",[1035],{"type":444,"value":646},{"type":444,"value":484},{"type":429,"tag":774,"props":1038,"children":1040},{"id":1039},"copy-neutral-loh-display-and-configuration",[1041],{"type":444,"value":1042},"Copy-neutral LOH, display and configuration",{"type":429,"tag":436,"props":1044,"children":1045},{},[1046],{"type":444,"value":1047},"Same as CNV, the copy-neutral LOH is displayed and configured the same way in both dense and expanded modes.",{"type":429,"tag":436,"props":1049,"children":1050},{},[1051],{"type":444,"value":1052},"Following example shows the somatic copy-neutral LOH of entire chromosome 17 in adrenal cortical tumors (ACT), retaining the mutant allele of the TP53 germline mutation R337H (blue x).",{"type":429,"tag":436,"props":1054,"children":1055},{},[1056],{"type":444,"value":1057},"To arrive at this view, you need to disable the LOH segment size limit by setting it to 0.",{"type":429,"tag":436,"props":1059,"children":1060},{},[1061],{"type":429,"tag":514,"props":1062,"children":1065},{"alt":1063,"src":1064},"img 17","/img/visualization-community/genomepaint/genomepaint-user-guide/image17.png",[],{"type":429,"tag":436,"props":1067,"children":1068},{},[1069],{"type":444,"value":1070},"The degree of LOH is determined by the \"seg.mean\" value, see the color scale in the legend:",{"type":429,"tag":436,"props":1072,"children":1073},{},[1074],{"type":429,"tag":514,"props":1075,"children":1078},{"alt":1076,"src":1077},"img 85","/img/visualization-community/genomepaint/genomepaint-user-guide/image85.png",[],{"type":429,"tag":436,"props":1080,"children":1081},{},[1082],{"type":444,"value":1083},"As in CNV, you can choose to show focal LOH using the segment size filter.\nYou can also set a minimum seg.mean value cutoff to drop low-value items.",{"type":429,"tag":774,"props":1085,"children":1087},{"id":1086},"sv-and-fusion-breakpoints-in-expanded-mode",[1088],{"type":444,"value":1089},"SV and fusion breakpoints in expanded mode",{"type":429,"tag":436,"props":1091,"children":1092},{},[1093],{"type":444,"value":1094},"In expanded mode, SV and fusion breakpoints are indicated by circles.\nA text label may be shown on the left or right of the circle.\nThe different colors represent translocating chromosomes, as indicated in legend.",{"type":429,"tag":436,"props":1096,"children":1097},{},[1098],{"type":444,"value":1099},"The occurrence of multiple breakpoints in a sample are indicated by multiple circles in the same row.",{"type":429,"tag":436,"props":1101,"children":1102},{},[1103,1105,1111],{"type":444,"value":1104},"Following example shows the translocation hotspot in ",{"type":429,"tag":1106,"props":1107,"children":1108},"em",{},[1109],{"type":444,"value":1110},"TCF3",{"type":444,"value":1112}," in BALL.\nThe text labels are shown for RNA fusion transcripts, but not genomic SV.",{"type":429,"tag":436,"props":1114,"children":1115},{},[1116],{"type":429,"tag":514,"props":1117,"children":1120},{"alt":1118,"src":1119},"img 26","/img/visualization-community/genomepaint/genomepaint-user-guide/image26.png",[],{"type":429,"tag":436,"props":1122,"children":1123},{},[1124],{"type":444,"value":1125},"Use the CONFIG menu to toggle the label visibility for SV and fusion separately.",{"type":429,"tag":436,"props":1127,"children":1128},{},[1129],{"type":429,"tag":514,"props":1130,"children":1133},{"alt":1131,"src":1132},"img 64","/img/visualization-community/genomepaint/genomepaint-user-guide/image64.png",[],{"type":429,"tag":774,"props":1135,"children":1137},{"id":1136},"snvindel-in-expanded-mode",[1138],{"type":444,"value":1139},"SNV/indel in expanded mode",{"type":429,"tag":436,"props":1141,"children":1142},{},[1143],{"type":444,"value":1144},"Here SNV/indels are represented as cross marks, using \"X\" for somatic mutations, and \"+\" for germline mutations.\nColors correspond to mutation class (mostly for coding mutations, see \"Mutation\" in legend).\nFor genic mutations, a HGVS styled label can be shown, as is generated by VEP.\nToggle label visibility in the CONFIG menu.",{"type":429,"tag":436,"props":1146,"children":1147},{},[1148],{"type":429,"tag":514,"props":1149,"children":1152},{"alt":1150,"src":1151},"img 16","/img/visualization-community/genomepaint/genomepaint-user-guide/image16.png",[],{"type":429,"tag":774,"props":1154,"children":1156},{"id":1155},"itd-in-the-expanded-mode",[1157],{"type":444,"value":1158},"ITD in the expanded mode",{"type":429,"tag":436,"props":1160,"children":1161},{},[1162],{"type":444,"value":1163},"ITD is represented as magenta bars over gene coding regions.",{"type":429,"tag":436,"props":1165,"children":1166},{},[1167],{"type":429,"tag":514,"props":1168,"children":1171},{"alt":1169,"src":1170},"img 12","/img/visualization-community/genomepaint/genomepaint-user-guide/image12.png",[],{"type":429,"tag":464,"props":1173,"children":1175},{"id":1174},"gene-expression",[1176],{"type":444,"value":1177},"Gene expression",{"type":429,"tag":436,"props":1179,"children":1180},{},[1181],{"type":444,"value":1182},"A subset of the pediatric tumors have gene expression profiled by RNA-Seq.\nGenomePaint supports displaying the following aspects of gene expression data:",{"type":429,"tag":531,"props":1184,"children":1185},{},[1186,1191,1196,1201],{"type":429,"tag":495,"props":1187,"children":1188},{},[1189],{"type":444,"value":1190},"Gene expression rank based on FPKM values",{"type":429,"tag":495,"props":1192,"children":1193},{},[1194],{"type":444,"value":1195},"Allele-specific expression status (ASE)",{"type":429,"tag":495,"props":1197,"children":1198},{},[1199],{"type":444,"value":1200},"Outlier high expression status",{"type":429,"tag":495,"props":1202,"children":1203},{},[1204],{"type":444,"value":1205},"RNA-Seq coverage and splice junctions (in Sample View)",{"type":429,"tag":774,"props":1207,"children":1209},{"id":1208},"expression-rank",[1210],{"type":444,"value":1211},"Expression rank",{"type":429,"tag":436,"props":1213,"children":1214},{},[1215],{"type":444,"value":1216},"This shows the ranking of gene expression in each sample, amongst all samples from the same cancer group:",{"type":429,"tag":531,"props":1218,"children":1219},{},[1220,1225],{"type":429,"tag":495,"props":1221,"children":1222},{},[1223],{"type":444,"value":1224},"Expression level from a neuroblastoma sample will be compared to expression of this gene in all neuroblastoma samples, but not expression from other cancers.",{"type":429,"tag":495,"props":1226,"children":1227},{},[1228],{"type":444,"value":1229},"All neuroblastoma samples with available expression data will be used to evaluate the ranking.",{"type":429,"tag":436,"props":1231,"children":1232},{},[1233],{"type":444,"value":1234},"Expression rankings are rendered as bar plots under the 0 to 100 scale, 0 for lowest among the group, 100 for highest.\nHover over a bar to see the actual rank, FPKM value, along with sample attributes.",{"type":429,"tag":436,"props":1236,"children":1237},{},[1238],{"type":429,"tag":514,"props":1239,"children":1242},{"alt":1240,"src":1241},"img 13","/img/visualization-community/genomepaint/genomepaint-user-guide/image13.png",[],{"type":429,"tag":436,"props":1244,"children":1245},{},[1246],{"type":444,"value":1247},"Blank row indicates either there is no expression data for selected gene from that sample, or the sample has no expression data at all.",{"type":429,"tag":1249,"props":1250,"children":1252},"h5",{"id":1251},"expression-rank-for-multiple-genes",[1253],{"type":444,"value":1254},"Expression rank for multiple genes",{"type":429,"tag":436,"props":1256,"children":1257},{},[1258,1260,1266],{"type":444,"value":1259},"It is possible to show expression rank for multiple genes like below.\nSee the section on ",{"type":429,"tag":476,"props":1261,"children":1263},{"href":1262},"#fixed-genes",[1264],{"type":444,"value":1265},"Fixed genes",{"type":444,"value":484},{"type":429,"tag":436,"props":1268,"children":1269},{},[1270],{"type":429,"tag":514,"props":1271,"children":1274},{"alt":1272,"src":1273},"img 69","/img/visualization-community/genomepaint/genomepaint-user-guide/image69.png",[],{"type":429,"tag":1249,"props":1276,"children":1278},{"id":1277},"find-expression-rank-when-there-are-no-genes-in-view-range",[1279],{"type":444,"value":1280},"Find expression rank when there are no genes in view range",{"type":429,"tag":436,"props":1282,"children":1283},{},[1284],{"type":444,"value":1285},"When there are no genes in view range, no expression ranking will be shown.\nIn its place, the \"ADD GENE\" phrase will be shown.",{"type":429,"tag":436,"props":1287,"children":1288},{},[1289],{"type":429,"tag":514,"props":1290,"children":1293},{"alt":1291,"src":1292},"img 65","/img/visualization-community/genomepaint/genomepaint-user-guide/image65.png",[],{"type":429,"tag":436,"props":1295,"children":1296},{},[1297],{"type":444,"value":1298},"Clicking \"ADD GENE\" to show a search box; type in gene name to search for a gene.",{"type":429,"tag":436,"props":1300,"children":1301},{},[1302],{"type":429,"tag":514,"props":1303,"children":1306},{"alt":1304,"src":1305},"img 72","/img/visualization-community/genomepaint/genomepaint-user-guide/image72.png",[],{"type":429,"tag":436,"props":1308,"children":1309},{},[1310],{"type":444,"value":1311},"By selecting a gene from the list, the expression ranking of this gene will be added.",{"type":429,"tag":436,"props":1313,"children":1314},{},[1315],{"type":429,"tag":514,"props":1316,"children":1319},{"alt":1317,"src":1318},"img 23","/img/visualization-community/genomepaint/genomepaint-user-guide/image23.png",[],{"type":429,"tag":436,"props":1321,"children":1322},{},[1323,1325,1329],{"type":444,"value":1324},"See the section ",{"type":429,"tag":476,"props":1326,"children":1327},{"href":1262},[1328],{"type":444,"value":1265},{"type":444,"value":1330}," for details.",{"type":429,"tag":774,"props":1332,"children":1334},{"id":1333},"allele-specific-expression-status-ase",[1335],{"type":444,"value":1195},{"type":429,"tag":436,"props":1337,"children":1338},{},[1339],{"type":444,"value":1340},"The pediatric tumor gene expression is annotated with the ASE status.\nThis is indicated using bar colors:",{"type":429,"tag":436,"props":1342,"children":1343},{},[1344],{"type":429,"tag":514,"props":1345,"children":1348},{"alt":1346,"src":1347},"ase legen","/img/visualization-community/genomepaint/genomepaint-user-guide/ase-legend.png",[],{"type":429,"tag":436,"props":1350,"children":1351},{},[1352],{"type":444,"value":1353},"Hover over a bar to see details about the ASE status.",{"type":429,"tag":436,"props":1355,"children":1356},{},[1357],{"type":429,"tag":514,"props":1358,"children":1361},{"alt":1359,"src":1360},"img 55","/img/visualization-community/genomepaint/genomepaint-user-guide/image55.png",[],{"type":429,"tag":436,"props":1363,"children":1364},{},[1365],{"type":444,"value":1366},"At the bottom of the tooltip, the ASE call is further explained with four fields:",{"type":429,"tag":531,"props":1368,"children":1369},{},[1370,1386,1402,1418],{"type":429,"tag":495,"props":1371,"children":1372},{},[1373,1378],{"type":429,"tag":440,"props":1374,"children":1375},{},[1376],{"type":444,"value":1377},"#SNPs heterozygous in DNA",{"type":429,"tag":531,"props":1379,"children":1380},{},[1381],{"type":429,"tag":495,"props":1382,"children":1383},{},[1384],{"type":444,"value":1385},"Total number of heterozygous SNPs in tumor genome over the gene body of this gene, as determined by tumor DNA sequencing",{"type":429,"tag":495,"props":1387,"children":1388},{},[1389,1394],{"type":429,"tag":440,"props":1390,"children":1391},{},[1392],{"type":444,"value":1393},"#SNPs showing ASE in RNA",{"type":429,"tag":531,"props":1395,"children":1396},{},[1397],{"type":429,"tag":495,"props":1398,"children":1399},{},[1400],{"type":444,"value":1401},"Number of such heterozygous markers showing mono-allelic expression.\nA binomial test with p-value cutoff is used to determine if one heterozygous SNP sufficiently deviates from 50%, if so this SNP is \"ASE\".\nThere should be 0 ASE SNPs for bi-allelic expressing genes, and >=1 for mono-allelic expressing genes.",{"type":429,"tag":495,"props":1403,"children":1404},{},[1405,1410],{"type":429,"tag":440,"props":1406,"children":1407},{},[1408],{"type":444,"value":1409},"Mean delta of ASE SNPs",{"type":429,"tag":531,"props":1411,"children":1412},{},[1413],{"type":429,"tag":495,"props":1414,"children":1415},{},[1416],{"type":444,"value":1417},"Mean value of (BAF-0.5) for all the markers. BAF: RNA B-allele frequency",{"type":429,"tag":495,"props":1419,"children":1420},{},[1421,1426],{"type":429,"tag":440,"props":1422,"children":1423},{},[1424],{"type":444,"value":1425},"Q-value",{"type":429,"tag":531,"props":1427,"children":1428},{},[1429],{"type":429,"tag":495,"props":1430,"children":1431},{},[1432],{"type":444,"value":1433},"First, the binomial p-values of all ASE SNPs for a gene are combined into one value using geometric mean; then, the combined p-values for all genes from a tumor are multiple-test corrected, to obtain this q-value for each gene.",{"type":429,"tag":436,"props":1435,"children":1436},{},[1437],{"type":444,"value":1438},"GenomePaint uses a decision tree to determine the ASE status of a gene in a sample (mono-allelic, bi-allelic, uncertain).\nTo customize the cutoff values, click the gene label and select \"Customize ASE/OHE parameters\":",{"type":429,"tag":436,"props":1440,"children":1441},{},[1442],{"type":429,"tag":514,"props":1443,"children":1446},{"alt":1444,"src":1445},"img 94","/img/visualization-community/genomepaint/genomepaint-user-guide/image94.png",[],{"type":429,"tag":436,"props":1448,"children":1449},{},[1450],{"type":444,"value":1451},"In the ASE decision tree, three cutoff values are customizable:",{"type":429,"tag":436,"props":1453,"children":1454},{},[1455],{"type":429,"tag":514,"props":1456,"children":1459},{"alt":1457,"src":1458},"img 34","/img/visualization-community/genomepaint/genomepaint-user-guide/image34.png",[],{"type":429,"tag":436,"props":1461,"children":1462},{},[1463],{"type":444,"value":1464},"For ASE, values for number of heterozygous SNPs, number of ASE SNPs, mean delta, and q-value are precomputed (Cis-X, Yu et. al., in submission) and cannot be recomputed on-the-fly.",{"type":429,"tag":774,"props":1466,"children":1468},{"id":1467},"automatic-genes",[1469],{"type":444,"value":1470},"\"Automatic\" genes",{"type":429,"tag":436,"props":1472,"children":1473},{},[1474,1476,1481],{"type":444,"value":1475},"While you pan and zoom the view range, genes update ",{"type":429,"tag":440,"props":1477,"children":1478},{},[1479],{"type":444,"value":1480},"automatically",{"type":444,"value":1482}," on the right in the expression column.\nIt always shows the first gene in the view range.",{"type":429,"tag":436,"props":1484,"children":1485},{},[1486],{"type":444,"value":1487},"When you zoom out and there are multiple genes in the view range, you may want to view some other gene rather than the default leftmost one.\nClick on the gene label on top of the rank axis and find a list of gene names from the view range.\nChoose a gene to change.\nBy choosing a gene here, whenever this gene is in the view range, it will always be shown irrespective of its order of appearance.",{"type":429,"tag":436,"props":1489,"children":1490},{},[1491],{"type":429,"tag":514,"props":1492,"children":1495},{"alt":1493,"src":1494},"img 4","/img/visualization-community/genomepaint/genomepaint-user-guide/image4.png",[],{"type":429,"tag":774,"props":1497,"children":1499},{"id":1498},"fixed-genes",[1500],{"type":444,"value":1501},"\"Fixed\" genes",{"type":429,"tag":436,"props":1503,"children":1504},{},[1505],{"type":444,"value":1506},"GenomePaint allows you to show the expression of multiple genes side-by-side:",{"type":429,"tag":436,"props":1508,"children":1509},{},[1510],{"type":429,"tag":514,"props":1511,"children":1514},{"alt":1512,"src":1513},"img 10","/img/visualization-community/genomepaint/genomepaint-user-guide/image10.png",[],{"type":429,"tag":436,"props":1516,"children":1517},{},[1518,1520,1525],{"type":444,"value":1519},"The gene on the left is \"automatic\".\nThe gene on right is added by user, and will be always shown irrespective of the view range, hence the ",{"type":429,"tag":440,"props":1521,"children":1522},{},[1523],{"type":444,"value":1524},"fixed genes",{"type":444,"value":484},{"type":429,"tag":436,"props":1527,"children":1528},{},[1529],{"type":444,"value":1530},"To add a fixed gene, click the gene label on top of the automatic expression rank axis to show the menu.\nType into the search box on top of the menu to find matching gene names:",{"type":429,"tag":436,"props":1532,"children":1533},{},[1534],{"type":429,"tag":514,"props":1535,"children":1538},{"alt":1536,"src":1537},"img 82","/img/visualization-community/genomepaint/genomepaint-user-guide/image82.png",[],{"type":429,"tag":436,"props":1540,"children":1541},{},[1542],{"type":444,"value":1543},"Select a gene from the list, and its expression rank will appear as a new column.\nMore than 1 fixed genes can be added.\nThe samples are aligned for both automatic and fixed genes.",{"type":429,"tag":436,"props":1545,"children":1546},{},[1547],{"type":444,"value":1548},"To remove a fixed gene, click the gene label and select \"Remove\".",{"type":429,"tag":436,"props":1550,"children":1551},{},[1552],{"type":429,"tag":514,"props":1553,"children":1556},{"alt":1554,"src":1555},"img 57","/img/visualization-community/genomepaint/genomepaint-user-guide/image57.png",[],{"type":429,"tag":436,"props":1558,"children":1559},{},[1560],{"type":444,"value":1561},"As an example, while browsing the recurrently duplicated NOTCH1 MYC enhancer locus in TALL, the distal target gene MYC is not in view range, thus its expression is not shown automatically.",{"type":429,"tag":436,"props":1563,"children":1564},{},[1565],{"type":429,"tag":514,"props":1566,"children":1569},{"alt":1567,"src":1568},"img 54","/img/visualization-community/genomepaint/genomepaint-user-guide/image54.png",[],{"type":429,"tag":436,"props":1571,"children":1572},{},[1573],{"type":444,"value":1574},"By adding MYC as a \"fixed gene\", its expression is shown for TALL tumors with enhancer duplication:",{"type":429,"tag":436,"props":1576,"children":1577},{},[1578],{"type":429,"tag":514,"props":1579,"children":1582},{"alt":1580,"src":1581},"img 3","/img/visualization-community/genomepaint/genomepaint-user-guide/image3.png",[],{"type":429,"tag":464,"props":1584,"children":1586},{"id":1585},"filters-for-samples-and-genomic-variants",[1587],{"type":444,"value":1588},"Filters for samples and genomic variants",{"type":429,"tag":436,"props":1590,"children":1591},{},[1592],{"type":444,"value":1593},"Here we introduce filters for samples and mutations in Cohort View.\nSome of these filters can be found in the track legend at the bottom of the page, where the filters are listed as legend entries.\nSome filters are hidden by default, click \"MORE\" at bottom to show them:",{"type":429,"tag":436,"props":1595,"children":1596},{},[1597],{"type":429,"tag":514,"props":1598,"children":1601},{"alt":1599,"src":1600},"img 76","/img/visualization-community/genomepaint/genomepaint-user-guide/image76.png",[],{"type":429,"tag":774,"props":1603,"children":1605},{"id":1604},"cancer-type-filter",[1606],{"type":444,"value":923},{"type":429,"tag":436,"props":1608,"children":1609},{},[1610],{"type":444,"value":1611},"In cohort view, one or more cancer types will be shown on the left of the mutation data display.\nClick on a cancer name to show a menu:",{"type":429,"tag":436,"props":1613,"children":1614},{},[1615],{"type":429,"tag":514,"props":1616,"children":1619},{"alt":1617,"src":1618},"img 43","/img/visualization-community/genomepaint/genomepaint-user-guide/image43.png",[],{"type":429,"tag":436,"props":1621,"children":1622},{},[1623],{"type":444,"value":1624},"Click \"Hide\" to hide samples of this cancer type; click \"Show only\" to only show samples of this cancer type.",{"type":429,"tag":436,"props":1626,"children":1627},{},[1628],{"type":444,"value":1629},"In the legend, hidden cancer types are indicated with a strikethrough; click a struck through label to turn it back on:",{"type":429,"tag":436,"props":1631,"children":1632},{},[1633],{"type":429,"tag":514,"props":1634,"children":1637},{"alt":1635,"src":1636},"img 37","/img/visualization-community/genomepaint/genomepaint-user-guide/image37.png",[],{"type":429,"tag":774,"props":1639,"children":1641},{"id":1640},"other-sample-filters",[1642],{"type":444,"value":1643},"Other sample filters",{"type":429,"tag":436,"props":1645,"children":1646},{},[1647],{"type":444,"value":1648},"You can filter samples by cancer group, sample type, gender, and race, in the same way as cancer type.",{"type":429,"tag":436,"props":1650,"children":1651},{},[1652],{"type":429,"tag":514,"props":1653,"children":1656},{"alt":1654,"src":1655},"img 73","/img/visualization-community/genomepaint/genomepaint-user-guide/image73.png",[],{"type":429,"tag":774,"props":1658,"children":1660},{"id":1659},"mutation-class-filter",[1661],{"type":444,"value":1662},"Mutation class filter",{"type":429,"tag":436,"props":1664,"children":1665},{},[1666],{"type":444,"value":1667},"Mutation class legend is shown as below.\nYou can select a class and hide it or show it only.",{"type":429,"tag":436,"props":1669,"children":1670},{},[1671],{"type":429,"tag":514,"props":1672,"children":1675},{"alt":1673,"src":1674},"img 44","/img/visualization-community/genomepaint/genomepaint-user-guide/image44.png",[],{"type":429,"tag":774,"props":1677,"children":1679},{"id":1678},"mutation-attribute-filter",[1680],{"type":444,"value":1681},"Mutation attribute filter",{"type":429,"tag":436,"props":1683,"children":1684},{},[1685],{"type":444,"value":1686},"Following are attributes describing mutations in each particular sample.\nUnlike mutation class which annotates a mutation no matter if it is germline or somatic, these attributes are assigned to mutations in each sample.",{"type":429,"tag":436,"props":1688,"children":1689},{},[1690],{"type":429,"tag":514,"props":1691,"children":1694},{"alt":1692,"src":1693},"img 48","/img/visualization-community/genomepaint/genomepaint-user-guide/image48.png",[],{"type":429,"tag":464,"props":1696,"children":1698},{"id":1697},"custom-sample-subsetting",[1699],{"type":444,"value":1700},"Custom sample subsetting",{"type":429,"tag":436,"props":1702,"children":1703},{},[1704],{"type":444,"value":1705},"In addition to grouping tumors with predefined cancer types, users can choose to limit the Cohort View to a custom defined sample subset.\nTo do that, click CONFIG, then select the \"Use a sample list\" button.",{"type":429,"tag":436,"props":1707,"children":1708},{},[1709],{"type":429,"tag":514,"props":1710,"children":1713},{"alt":1711,"src":1712},"img 6","/img/visualization-community/genomepaint/genomepaint-user-guide/image6.png",[],{"type":429,"tag":436,"props":1715,"children":1716},{},[1717],{"type":444,"value":1718},"An input box is displayed prompting the user to enter the set of samples.",{"type":429,"tag":436,"props":1720,"children":1721},{},[1722],{"type":429,"tag":514,"props":1723,"children":1726},{"alt":1724,"src":1725},"img 14","/img/visualization-community/genomepaint/genomepaint-user-guide/image14.png",[],{"type":429,"tag":436,"props":1728,"children":1729},{},[1730],{"type":444,"value":1731},"For the moment, space character is reserved for dividing the sample and group names, and cannot be used in either sample or group name.",{"type":429,"tag":436,"props":1733,"children":1734},{},[1735],{"type":444,"value":1736},"As an example, use the following list of samples that are divided into two groups.",{"type":429,"tag":1738,"props":1739,"children":1742},"pre",{"className":1740,"code":1741,"language":444,"meta":424,"style":424},"language-text shiki shiki-themes material-theme-lighter material-theme material-theme-palenight","SJTALL002030_D1-PARVHY T-ALLs\nSJALL015249_D1-PARPHB T-ALLs\nSJALL015260_D1-PARMKK T-ALLs\nSJALL015268_D1-PASFHR T-ALLs\nSJALL015278_D1-PARJPL T-ALLs\nSJALL015280_D1-PARNMV T-ALLs\nSJALL015285_D1-PASKTG T-ALLs\nSJTALL002072_D1-PATHJF T-ALLs\nSJALL015269_D1-PASFKA T-ALLs\nSJBALL020492_D2-PANKGK B-ALLs\nSJERG009_D B-ALLs\nSJPHALL006_D B-ALLs\nSJBALL020795_D2-PAPIRZ B-ALLs\nSJETV088_D B-ALLs\nSJHYPER143_D B-ALLs\nSJETV059_D B-ALLs\nSJETV069_D B-ALLs\nSJHYPER052_D B-ALLs\nSJBALL020469_D1 B-ALLs\nSJHYPER013_D B-ALLs\n",[1743],{"type":429,"tag":1744,"props":1745,"children":1746},"code",{"__ignoreMap":424},[1747,1758,1767,1776,1785,1794,1803,1812,1821,1830,1839,1848,1857,1866,1875,1884,1893,1902,1911,1920],{"type":429,"tag":1748,"props":1749,"children":1752},"span",{"class":1750,"line":1751},"line",1,[1753],{"type":429,"tag":1748,"props":1754,"children":1755},{},[1756],{"type":444,"value":1757},"SJTALL002030_D1-PARVHY T-ALLs\n",{"type":429,"tag":1748,"props":1759,"children":1761},{"class":1750,"line":1760},2,[1762],{"type":429,"tag":1748,"props":1763,"children":1764},{},[1765],{"type":444,"value":1766},"SJALL015249_D1-PARPHB T-ALLs\n",{"type":429,"tag":1748,"props":1768,"children":1770},{"class":1750,"line":1769},3,[1771],{"type":429,"tag":1748,"props":1772,"children":1773},{},[1774],{"type":444,"value":1775},"SJALL015260_D1-PARMKK T-ALLs\n",{"type":429,"tag":1748,"props":1777,"children":1779},{"class":1750,"line":1778},4,[1780],{"type":429,"tag":1748,"props":1781,"children":1782},{},[1783],{"type":444,"value":1784},"SJALL015268_D1-PASFHR T-ALLs\n",{"type":429,"tag":1748,"props":1786,"children":1788},{"class":1750,"line":1787},5,[1789],{"type":429,"tag":1748,"props":1790,"children":1791},{},[1792],{"type":444,"value":1793},"SJALL015278_D1-PARJPL T-ALLs\n",{"type":429,"tag":1748,"props":1795,"children":1797},{"class":1750,"line":1796},6,[1798],{"type":429,"tag":1748,"props":1799,"children":1800},{},[1801],{"type":444,"value":1802},"SJALL015280_D1-PARNMV T-ALLs\n",{"type":429,"tag":1748,"props":1804,"children":1806},{"class":1750,"line":1805},7,[1807],{"type":429,"tag":1748,"props":1808,"children":1809},{},[1810],{"type":444,"value":1811},"SJALL015285_D1-PASKTG T-ALLs\n",{"type":429,"tag":1748,"props":1813,"children":1815},{"class":1750,"line":1814},8,[1816],{"type":429,"tag":1748,"props":1817,"children":1818},{},[1819],{"type":444,"value":1820},"SJTALL002072_D1-PATHJF T-ALLs\n",{"type":429,"tag":1748,"props":1822,"children":1824},{"class":1750,"line":1823},9,[1825],{"type":429,"tag":1748,"props":1826,"children":1827},{},[1828],{"type":444,"value":1829},"SJALL015269_D1-PASFKA T-ALLs\n",{"type":429,"tag":1748,"props":1831,"children":1833},{"class":1750,"line":1832},10,[1834],{"type":429,"tag":1748,"props":1835,"children":1836},{},[1837],{"type":444,"value":1838},"SJBALL020492_D2-PANKGK B-ALLs\n",{"type":429,"tag":1748,"props":1840,"children":1842},{"class":1750,"line":1841},11,[1843],{"type":429,"tag":1748,"props":1844,"children":1845},{},[1846],{"type":444,"value":1847},"SJERG009_D B-ALLs\n",{"type":429,"tag":1748,"props":1849,"children":1851},{"class":1750,"line":1850},12,[1852],{"type":429,"tag":1748,"props":1853,"children":1854},{},[1855],{"type":444,"value":1856},"SJPHALL006_D B-ALLs\n",{"type":429,"tag":1748,"props":1858,"children":1860},{"class":1750,"line":1859},13,[1861],{"type":429,"tag":1748,"props":1862,"children":1863},{},[1864],{"type":444,"value":1865},"SJBALL020795_D2-PAPIRZ B-ALLs\n",{"type":429,"tag":1748,"props":1867,"children":1869},{"class":1750,"line":1868},14,[1870],{"type":429,"tag":1748,"props":1871,"children":1872},{},[1873],{"type":444,"value":1874},"SJETV088_D B-ALLs\n",{"type":429,"tag":1748,"props":1876,"children":1878},{"class":1750,"line":1877},15,[1879],{"type":429,"tag":1748,"props":1880,"children":1881},{},[1882],{"type":444,"value":1883},"SJHYPER143_D B-ALLs\n",{"type":429,"tag":1748,"props":1885,"children":1887},{"class":1750,"line":1886},16,[1888],{"type":429,"tag":1748,"props":1889,"children":1890},{},[1891],{"type":444,"value":1892},"SJETV059_D B-ALLs\n",{"type":429,"tag":1748,"props":1894,"children":1896},{"class":1750,"line":1895},17,[1897],{"type":429,"tag":1748,"props":1898,"children":1899},{},[1900],{"type":444,"value":1901},"SJETV069_D B-ALLs\n",{"type":429,"tag":1748,"props":1903,"children":1905},{"class":1750,"line":1904},18,[1906],{"type":429,"tag":1748,"props":1907,"children":1908},{},[1909],{"type":444,"value":1910},"SJHYPER052_D B-ALLs\n",{"type":429,"tag":1748,"props":1912,"children":1914},{"class":1750,"line":1913},19,[1915],{"type":429,"tag":1748,"props":1916,"children":1917},{},[1918],{"type":444,"value":1919},"SJBALL020469_D1 B-ALLs\n",{"type":429,"tag":1748,"props":1921,"children":1923},{"class":1750,"line":1922},20,[1924],{"type":429,"tag":1748,"props":1925,"children":1926},{},[1927],{"type":444,"value":1928},"SJHYPER013_D B-ALLs\n",{"type":429,"tag":436,"props":1930,"children":1931},{},[1932],{"type":444,"value":1933},"The Cohort View will be transformed to showing only these samples in two groups:",{"type":429,"tag":436,"props":1935,"children":1936},{},[1937],{"type":429,"tag":514,"props":1938,"children":1941},{"alt":1939,"src":1940},"img 83","/img/visualization-community/genomepaint/genomepaint-user-guide/image83.png",[],{"type":429,"tag":436,"props":1943,"children":1944},{},[1945],{"type":444,"value":1946},"Click a group label to see options:",{"type":429,"tag":436,"props":1948,"children":1949},{},[1950],{"type":429,"tag":514,"props":1951,"children":1954},{"alt":1952,"src":1953},"img 86","/img/visualization-community/genomepaint/genomepaint-user-guide/image86.png",[],{"type":429,"tag":436,"props":1956,"children":1957},{},[1958],{"type":444,"value":1959},"After submission, a sample set can be edited.\nTo do that, inside the CONFIG menu click on the \"Edit\" button following the \"Restricted to xx samples\" phrase, and open the same input box allowing to edit the list of samples.",{"type":429,"tag":436,"props":1961,"children":1962},{},[1963],{"type":429,"tag":514,"props":1964,"children":1967},{"alt":1965,"src":1966},"img 74","/img/visualization-community/genomepaint/genomepaint-user-guide/image74.png",[],{"type":429,"tag":436,"props":1969,"children":1970},{},[1971],{"type":444,"value":1972},"Click on the \"Remove\" button to cancel the sample subsetting and go back to full Cohort View.",{"type":429,"tag":436,"props":1974,"children":1975},{},[1976],{"type":444,"value":1977},"Sample subsetting can be applied to custom track as well.",{"type":429,"tag":464,"props":1979,"children":1981},{"id":1980},"assay-availability-table",[1982],{"type":444,"value":1983},"Assay availability table",{"type":429,"tag":436,"props":1985,"children":1986},{},[1987],{"type":444,"value":1988},"The Pediatric cancer dataset is equipped with a feature to show assay availability information for each cancer type.\nThis is important in providing a precise total sample count based on assay type.",{"type":429,"tag":436,"props":1990,"children":1991},{},[1992],{"type":444,"value":1993},"As an example, T-ALL displays 78 samples with alterations at the TAL1 locus.\nThe \"21%\" percentage is imprecise and only servers as a rough guide, as it doesn't account for assay availability.",{"type":429,"tag":436,"props":1995,"children":1996},{},[1997],{"type":429,"tag":514,"props":1998,"children":2001},{"alt":1999,"src":2000},"img 70","/img/visualization-community/genomepaint/genomepaint-user-guide/image70.png",[],{"type":429,"tag":436,"props":2003,"children":2004},{},[2005],{"type":444,"value":2006},"The track legend shows two DNA assay types for these alterations: SNP6 and \"amplicon sequencing\".\nIn addition there are also fusion events from RNA-Seq.\nThus, to compute the percentage of T-ALLs with TAL1 locus alteration, one needs the total number of T-ALLs with either SNP6, amplicon sequencing, or RNA-Seq.\nTo get the actual total number, click the \"HM, TALL\" label on the left and select \"Assay summary\" option.",{"type":429,"tag":436,"props":2008,"children":2009},{},[2010],{"type":429,"tag":514,"props":2011,"children":2014},{"alt":2012,"src":2013},"img 31","/img/visualization-community/genomepaint/genomepaint-user-guide/image31.png",[],{"type":429,"tag":436,"props":2016,"children":2017},{},[2018],{"type":444,"value":2019},"The assay availability for T-ALL is displayed as a map below.",{"type":429,"tag":436,"props":2021,"children":2022},{},[2023],{"type":429,"tag":514,"props":2024,"children":2027},{"alt":2025,"src":2026},"img 36","/img/visualization-community/genomepaint/genomepaint-user-guide/image36.png",[],{"type":429,"tag":436,"props":2029,"children":2030},{},[2031],{"type":444,"value":2032},"The map is an assay-by-sample matrix, with assays as rows and samples as columns.\nAll assays available for T-ALLs are included.\nBy default, the assays are arranged from top to bottom in descending order of sample counts (RNA and WES being the most abundant).\nInside the matrix, a gray box indicates a set of samples having a particular assay type.\nThe number of samples are always printed out for each box.",{"type":429,"tag":436,"props":2034,"children":2035},{},[2036],{"type":444,"value":2037},"The sample columns are sorted by the presence of each assay type, by the order of assays from top to bottom.\nIn the T-ALL case, the samples are first sorted by RNA-Seq, with 267 that have RNA-Seq and 86 without (number not printed).\nNext, WES availability is sorted separately for the box and blank from the first row, resulting in two boxes and two blanks.\nNext, the SNP6 availability is sorted separately in each box and blank in the second row.\nSo on for every other assay type.\nImportantly, the width of the gray boxes are not scaled by the number of samples, but rather symbolic representations of the cohort partitioning.\nThough not to scale, the boxes are vertically aligned with columns being groups of samples.\nBetter than a Venn diagram, this assay availability map solidifies a comprehensible view with as many as 6 assay types.",{"type":429,"tag":436,"props":2039,"children":2040},{},[2041],{"type":444,"value":2042},"As the order of assay types is important for the map, users can adjust the row order by dragging a label up or down.\nAs below, the RNA-Seq, SNP6, and Capture-seq rows are moved to the top, yielding a total of 337 samples (267+70) for the samples with TAL1 locus alterations.",{"type":429,"tag":436,"props":2044,"children":2045},{},[2046],{"type":429,"tag":514,"props":2047,"children":2050},{"alt":2048,"src":2049},"img 18","/img/visualization-community/genomepaint/genomepaint-user-guide/image18.png",[],{"type":429,"tag":464,"props":2052,"children":2054},{"id":2053},"kaplan-meier-plot",[2055],{"type":444,"value":2056},"Kaplan-Meier plot",{"type":429,"tag":436,"props":2058,"children":2059},{},[2060],{"type":444,"value":2061},"Patient outcome (event-free and overall survival) information is available for 1102 samples (6 histotypes) from the \"Pan-TARGET\" study (Ma, X. et al. Nature 2018).\nGenomePaint provides following ways to stratify this cohort using genomic alteration or gene expression, and to perform the Kaplan-Meier analysis to assess what clinical outcome does the genomic feature lead to.\nThe analysis will compute the p value using the G-rho family of tests (the \"survdiff\" function in R), as well as plotting the survival curves.",{"type":429,"tag":436,"props":2063,"children":2064},{},[2065],{"type":444,"value":2066},"Kaplan-Meier analysis is performed on each individual cancer type.",{"type":429,"tag":774,"props":2068,"children":2070},{"id":2069},"with-genomic-alterations",[2071],{"type":444,"value":2072},"With genomic alterations",{"type":429,"tag":436,"props":2074,"children":2075},{},[2076],{"type":444,"value":2077},"This usually applies to recurrent mutations/alterations, or frequently mutated regions, as sufficient number of mutated samples may be required for the analysis.",{"type":429,"tag":1249,"props":2079,"children":2081},{"id":2080},"with-a-specific-mutationalteration",[2082],{"type":444,"value":2083},"With a specific mutation/alteration",{"type":429,"tag":436,"props":2085,"children":2086},{},[2087],{"type":444,"value":2088},"CDKN2A/2B is recurrently deleted in acute lymphoblastic leukemia.\nTo see how this deletion may impact clinical outcome, visit CDKN2A locus in GenomePaint, and select a deletion spanning the locus to show a panel (left).\nOn top of this panel, select the \"Survival plot\".\nThis will use the range of this particular deletion to stratify tumors: samples with deletions overlapping with this range will be separated from samples that don't.\nAs a result, a survival curve like below can be shown for BALL.",{"type":429,"tag":436,"props":2090,"children":2091},{},[2092],{"type":429,"tag":514,"props":2093,"children":2096},{"alt":2094,"src":2095},"img 78","/img/visualization-community/genomepaint/genomepaint-user-guide/image78.png",[],{"type":429,"tag":436,"props":2098,"children":2099},{},[2100],{"type":444,"value":2101},"Such procedure can be applied to other types of mutation/alteration as well.\nIf a CNV is selected, samples may be divided to up to three groups (gain, loss, no change).\nIf any other type of alteration is selected, samples will be divided into just two groups (with mutation, no mutation).",{"type":429,"tag":1249,"props":2103,"children":2105},{"id":2104},"with-any-alterations-from-a-chosen-genomic-interval",[2106],{"type":444,"value":2107},"With any alterations from a chosen genomic interval",{"type":429,"tag":436,"props":2109,"children":2110},{},[2111],{"type":444,"value":2112},"MYB is subject to multiple types of genomic alterations in TALL, including amplification, activating mutation, intragenic and intergenic translocations.\nTo collectively consider the effect of these alterations on TALL patient outcome, view data in the range chr6:135482339-135674218 (hg19), a 190 Kb region around MYB, which will include coding mutations, amplification, and intergenic translocations that have been found to cause MYB activation.\nThen, click on the \"HM, TALL\" label on the left and select the \"Survival plot\" option.\nThis will select TALL patients with any variant in the view range into the \"mutated\" group, for comparing with the \"no mutation\" group in the Kaplan-Meier analysis.",{"type":429,"tag":436,"props":2114,"children":2115},{},[2116],{"type":429,"tag":514,"props":2117,"children":2120},{"alt":2118,"src":2119},"img 50","/img/visualization-community/genomepaint/genomepaint-user-guide/image50.png",[],{"type":429,"tag":436,"props":2122,"children":2123},{},[2124,2126,2132],{"type":444,"value":2125},"CNV, LOH parameter settings and ",{"type":429,"tag":476,"props":2127,"children":2129},{"href":2128},"#mutation-class-filter",[2130],{"type":444,"value":2131},"mutation class filter",{"type":444,"value":2133}," will be applied to filter alteration events in the survival plot.",{"type":429,"tag":774,"props":2135,"children":2137},{"id":2136},"with-fpkm-values-of-a-chosen-gene",[2138],{"type":444,"value":2139},"With FPKM values of a chosen gene",{"type":429,"tag":436,"props":2141,"children":2142},{},[2143],{"type":444,"value":2144},"MDM2 overexpression may lead to shortened half-life of P53 protein, thus may lead to worse outcome in cancer patients.\nTo test this hypothesis, show MDM2 in GenomePaint.\nOn the right of gene expression rank plot, click \"MDM2\" label, then select \"Survival plot by MDM2 FPKM\".",{"type":429,"tag":436,"props":2146,"children":2147},{},[2148],{"type":429,"tag":514,"props":2149,"children":2152},{"alt":2150,"src":2151},"img 11","/img/visualization-community/genomepaint/genomepaint-user-guide/image11.png",[],{"type":429,"tag":436,"props":2154,"children":2155},{},[2156],{"type":444,"value":2157},"This will perform the analysis on BALL by default, using MDM2 median expression as cutoff to divide the samples to two groups.\nSwitch the cancer type to AML, and median into quartile, to view the plot showing high MDM2 expression is correlated with worse outcome in AML.",{"type":429,"tag":436,"props":2159,"children":2160},{},[2161],{"type":429,"tag":514,"props":2162,"children":2165},{"alt":2163,"src":2164},"img 63","/img/visualization-community/genomepaint/genomepaint-user-guide/image63.png",[],{"type":429,"tag":453,"props":2167,"children":2169},{"id":2168},"sample-view",[2170],{"type":444,"value":646},{"type":429,"tag":436,"props":2172,"children":2173},{},[2174],{"type":444,"value":2175},"From Cohort View, click any type of mutation to show a panel; at the left of this panel, click the \"Sample View\" button to show a new browser view showing data tracks from this sample in a region surrounding the mutation:",{"type":429,"tag":436,"props":2177,"children":2178},{},[2179],{"type":429,"tag":514,"props":2180,"children":2183},{"alt":2181,"src":2182},"img 88","/img/visualization-community/genomepaint/genomepaint-user-guide/image88.png",[],{"type":429,"tag":464,"props":2185,"children":2187},{"id":2186},"pediatric-tumors-in-sample-view",[2188],{"type":444,"value":2189},"Pediatric tumors in Sample View",{"type":429,"tag":774,"props":2191,"children":2193},{"id":2192},"mutation-data-in-sample-view",[2194],{"type":444,"value":2195},"Mutation data in Sample View",{"type":429,"tag":436,"props":2197,"children":2198},{},[2199,2201,2207],{"type":444,"value":2200},"The Sample View shows a number of tracks, one of them is the mutations, named \"Pediatric tumor mutation, ",{"type":429,"tag":1744,"props":2202,"children":2204},{"className":2203},[],[2205],{"type":444,"value":2206},"\u003Cname of this sample>",{"type":444,"value":2208},"\".\nIn the example below, a Wilms' tumor shows 4 different types of mutations over the MYCN gene, including copy number gain, LOH (not copy-neutral), SV supporting this CNV, and a coding mutation in MYCN.",{"type":429,"tag":436,"props":2210,"children":2211},{},[2212],{"type":429,"tag":514,"props":2213,"children":2216},{"alt":2214,"src":2215},"img 47","/img/visualization-community/genomepaint/genomepaint-user-guide/image47.png",[],{"type":429,"tag":774,"props":2218,"children":2220},{"id":2219},"mutation-signature",[2221],{"type":444,"value":2222},"Mutation signature",{"type":429,"tag":436,"props":2224,"children":2225},{},[2226],{"type":444,"value":2227},"In the above example, the missense mutation is colored in green because of its mutation signature assignment in that sample.",{"type":429,"tag":436,"props":2229,"children":2230},{},[2231],{"type":429,"tag":514,"props":2232,"children":2235},{"alt":2233,"src":2234},"img 66","/img/visualization-community/genomepaint/genomepaint-user-guide/image66.png",[],{"type":429,"tag":436,"props":2237,"children":2238},{},[2239],{"type":444,"value":2240},"Mutation signature is available for 915 tumors from the Pan-TARGET study (Ma, X et al. Nature 2018).\nFor such tumors, their mutations in Sample View will be colored by assigned signatures.\nUsers can also view the mutation signature abundance for a sample by clicking the \"Mutation signature\" button on top.",{"type":429,"tag":436,"props":2242,"children":2243},{},[2244],{"type":429,"tag":514,"props":2245,"children":2248},{"alt":2246,"src":2247},"img 60","/img/visualization-community/genomepaint/genomepaint-user-guide/image60.png",[],{"type":429,"tag":774,"props":2250,"children":2252},{"id":2251},"multi-region-display-for-inter-chromosomal-sv",[2253],{"type":444,"value":2254},"Multi-region display for inter-chromosomal SV",{"type":429,"tag":436,"props":2256,"children":2257},{},[2258],{"type":444,"value":2259},"When a user clicks on an inter-chromosomal SV and launches Sample View, the view will contain a pair of regions each containing one breakpoint, from two chromosomes.\nRegions are spaced by a vertical gray bar.\nThe following example shows a pair of genomic regions upon clicking the ETV6-ABL1 fusion transcript in a TALL sample; the left region with ETV6 is chr12, and the right-side region with ABL1 is chr9.",{"type":429,"tag":436,"props":2261,"children":2262},{},[2263],{"type":429,"tag":514,"props":2264,"children":2267},{"alt":2265,"src":2266},"img 25","/img/visualization-community/genomepaint/genomepaint-user-guide/image25.png",[],{"type":429,"tag":436,"props":2269,"children":2270},{},[2271],{"type":444,"value":2272},"To zoom in on either region, drag on the coordinate ruler on top of one region.",{"type":429,"tag":436,"props":2274,"children":2275},{},[2276],{"type":444,"value":2277},"To zoom out on the left-side region, click the \"zoom out\" buttons.",{"type":429,"tag":436,"props":2279,"children":2280},{},[2281],{"type":444,"value":2282},"To zoom out on the right-side region, instead of clicking on the \"zoom out\" buttons, hover and show an option on top, click that option to zoom the right-side region.",{"type":429,"tag":436,"props":2284,"children":2285},{},[2286],{"type":429,"tag":514,"props":2287,"children":2290},{"alt":2288,"src":2289},"img 2","/img/visualization-community/genomepaint/genomepaint-user-guide/image2.png",[],{"type":429,"tag":774,"props":2292,"children":2294},{"id":2293},"sequencing-coverage-and-allelic-imbalance-tracks-in-single-sample-view",[2295],{"type":444,"value":2296},"Sequencing coverage and allelic-imbalance tracks in single-sample view",{"type":429,"tag":436,"props":2298,"children":2299},{},[2300],{"type":444,"value":2301},"GenomePaint aims to provide comprehensive genomics information to assist in interpreting mutations from individual tumors.\nThis includes additional genomic assay tracks on individual tumors if they are available to us.\nFollowing is a typical example:",{"type":429,"tag":436,"props":2303,"children":2304},{},[2305],{"type":429,"tag":514,"props":2306,"children":2309},{"alt":2307,"src":2308},"img 61","/img/visualization-community/genomepaint/genomepaint-user-guide/image61.png",[],{"type":429,"tag":436,"props":2311,"children":2312},{},[2313],{"type":444,"value":2314},"In the above example, it shows coverage of WGS and RNA-Seq of tumor, and the allelic-imbalance from the tumor-normal paired WGS results.",{"type":429,"tag":436,"props":2316,"children":2317},{},[2318,2325],{"type":429,"tag":476,"props":2319,"children":2322},{"href":2320,"rel":2321},"https://docs.google.com/document/d/1dZIOoLLbQE-kmZ31Ia_5cud30d9UeRodP4hRCSw3HII/edit?usp=sharing",[480],[2323],{"type":444,"value":2324},"Learn more about the allelic-imbalance track",{"type":444,"value":484},{"type":429,"tag":464,"props":2327,"children":2329},{"id":2328},"hi-c-data-from-pediatric-cancer-cell-lines",[2330],{"type":444,"value":2331},"Hi-C data from pediatric cancer cell lines",{"type":429,"tag":436,"props":2333,"children":2334},{},[2335],{"type":444,"value":2336},"GenomePaint provides the detailed genomic and epigenomic assaying results of a set of pediatric cancer cell lines to supplement the primary tumor mutation dataset.\nCurrently there are six neuroblastoma cell lines (SKNAS, NB69, Kelly, BE2C, NGP, SH-SY5Y) and one BALL cell line (NALM6), all grouped with primary tumors of the same cancer type.\nWhen a cell line appears in the genomic mutation data panel, it will be marked by a black notch on left:",{"type":429,"tag":436,"props":2338,"children":2339},{},[2340],{"type":429,"tag":514,"props":2341,"children":2344},{"alt":2342,"src":2343},"img 56","/img/visualization-community/genomepaint/genomepaint-user-guide/image56.png",[],{"type":429,"tag":436,"props":2346,"children":2347},{},[2348],{"type":444,"value":2349},"These cell lines all come with in-situ Hi-C data, in addition to the histone modification ChIP-seq.\nThese tracks will be shown in the single-sample view of these cell lines.",{"type":429,"tag":436,"props":2351,"children":2352},{},[2353],{"type":429,"tag":514,"props":2354,"children":2357},{"alt":2355,"src":2356},"img 19","/img/visualization-community/genomepaint/genomepaint-user-guide/image19.png",[],{"type":429,"tag":436,"props":2359,"children":2360},{},[2361,2368],{"type":429,"tag":476,"props":2362,"children":2365},{"href":2363,"rel":2364},"https://docs.google.com/document/d/1MQ0Z_AD5moDmaSx2tcn7DyVKGp49TS63pO0cceGL_Ns/edit?usp=sharing",[480],[2366],{"type":444,"value":2367},"Learn more about the Hi-C track",{"type":444,"value":484},{"type":429,"tag":453,"props":2370,"children":2372},{"id":2371},"matrix-view",[2373],{"type":444,"value":653},{"type":429,"tag":436,"props":2375,"children":2376},{},[2377],{"type":444,"value":2378},"Matrix View is a light-weight method for combining multiple genomic regions into one view so as to compare their mutational profiles over a group of samples, via a sample-by-region matrix:",{"type":429,"tag":436,"props":2380,"children":2381},{},[2382],{"type":429,"tag":514,"props":2383,"children":2386},{"alt":2384,"src":2385},"img 90","/img/visualization-community/genomepaint/genomepaint-user-guide/image90.png",[],{"type":429,"tag":436,"props":2388,"children":2389},{},[2390],{"type":444,"value":2391},"Such a matrix can be generated for samples from one cancer type.\nFollowing demonstrates how to use the Matrix View to observe the MYCN-ATRX mutual exclusivity in neuroblastoma.",{"type":429,"tag":436,"props":2393,"children":2394},{},[2395],{"type":444,"value":2396},"First, show the NBL mutation profile at the MYCN locus.",{"type":429,"tag":436,"props":2398,"children":2399},{},[2400],{"type":429,"tag":514,"props":2401,"children":2404},{"alt":2402,"src":2403},"img 46","/img/visualization-community/genomepaint/genomepaint-user-guide/image46.png",[],{"type":429,"tag":436,"props":2406,"children":2407},{},[2408],{"type":444,"value":2409},"By default MYCNOS gene is showing for the expression rank, change it to MYCN.\nThis can allow the region to be named as \"MYCN\" rather than \"MYCNOS\" in the Matrix View.",{"type":429,"tag":436,"props":2411,"children":2412},{},[2413],{"type":429,"tag":514,"props":2414,"children":2417},{"alt":2415,"src":2416},"img 49","/img/visualization-community/genomepaint/genomepaint-user-guide/image49.png",[],{"type":429,"tag":436,"props":2419,"children":2420},{},[2421],{"type":444,"value":2422},"Click on the \"ST, NBL\" label on left, and select \"Matrix view\".",{"type":429,"tag":436,"props":2424,"children":2425},{},[2426],{"type":429,"tag":514,"props":2427,"children":2430},{"alt":2428,"src":2429},"img 29","/img/visualization-community/genomepaint/genomepaint-user-guide/image29.png",[],{"type":429,"tag":436,"props":2432,"children":2433},{},[2434],{"type":444,"value":2435},"This gathers the group of NBL tumors with mutations in MYCN into a single-column matrix.",{"type":429,"tag":436,"props":2437,"children":2438},{},[2439],{"type":429,"tag":514,"props":2440,"children":2443},{"alt":2441,"src":2442},"img 45","/img/visualization-community/genomepaint/genomepaint-user-guide/image45.png",[],{"type":429,"tag":436,"props":2445,"children":2446},{},[2447],{"type":444,"value":2448},"Back to the Cohort View.\nType \"atrx\" into the coordinate box and press ENTER.",{"type":429,"tag":436,"props":2450,"children":2451},{},[2452],{"type":429,"tag":514,"props":2453,"children":2456},{"alt":2454,"src":2455},"img 8","/img/visualization-community/genomepaint/genomepaint-user-guide/image8.png",[],{"type":429,"tag":436,"props":2458,"children":2459},{},[2460],{"type":444,"value":2461},"Cohort View now shows ATRX mutations from NBL.\nClick the \"ST, NBL\" label on the left, and select \"Matrix View\".",{"type":429,"tag":436,"props":2463,"children":2464},{},[2465],{"type":429,"tag":514,"props":2466,"children":2469},{"alt":2467,"src":2468},"img 30","/img/visualization-community/genomepaint/genomepaint-user-guide/image30.png",[],{"type":429,"tag":436,"props":2471,"children":2472},{},[2473],{"type":444,"value":2474},"This will add ATRX as a new column alongside MYCN in the Matrix View.\nIt shows that the majority of NBL tumors only display alteration at one gene.",{"type":429,"tag":436,"props":2476,"children":2477},{},[2478],{"type":429,"tag":514,"props":2479,"children":2482},{"alt":2480,"src":2481},"img 1","/img/visualization-community/genomepaint/genomepaint-user-guide/image1.png",[],{"type":429,"tag":453,"props":2484,"children":2486},{"id":2485},"custom-track",[2487],{"type":444,"value":2488},"Custom track",{"type":429,"tag":464,"props":2490,"children":2492},{"id":2491},"feature-availability",[2493],{"type":444,"value":2494},"Feature availability",{"type":429,"tag":436,"props":2496,"children":2497},{},[2498],{"type":444,"value":2499},"Features available for custom track:",{"type":429,"tag":531,"props":2501,"children":2502},{},[2503,2508,2513,2518,2546,2569,2574,2579],{"type":429,"tag":495,"props":2504,"children":2505},{},[2506],{"type":444,"value":2507},"All types of mutations are supported, including SNV/indel, CNV, LOH, SV, fusion, ITD.",{"type":429,"tag":495,"props":2509,"children":2510},{},[2511],{"type":444,"value":2512},"Gene expression FPKM values and ranking are supported, together with ASE status.",{"type":429,"tag":495,"props":2514,"children":2515},{},[2516],{"type":444,"value":2517},"Customizing ASE parameters.",{"type":429,"tag":495,"props":2519,"children":2520},{},[2521,2523],{"type":444,"value":2522},"Cohort View:\n",{"type":429,"tag":531,"props":2524,"children":2525},{},[2526,2531,2536,2541],{"type":429,"tag":495,"props":2527,"children":2528},{},[2529],{"type":444,"value":2530},"Showing mutation profile.",{"type":429,"tag":495,"props":2532,"children":2533},{},[2534],{"type":444,"value":2535},"Mutation annotation with user-defined attributes; this is for display only and cannot be used for filtering.",{"type":429,"tag":495,"props":2537,"children":2538},{},[2539],{"type":444,"value":2540},"Computing and displaying gene expression rank among all samples.",{"type":429,"tag":495,"props":2542,"children":2543},{},[2544],{"type":444,"value":2545},"Custom sample subsetting.",{"type":429,"tag":495,"props":2547,"children":2548},{},[2549,2551],{"type":444,"value":2550},"Sample View:\n",{"type":429,"tag":531,"props":2552,"children":2553},{},[2554,2559,2564],{"type":429,"tag":495,"props":2555,"children":2556},{},[2557],{"type":444,"value":2558},"Displaying mutation track, as well as multi-region view triggered by inter-chromosomal SV.",{"type":429,"tag":495,"props":2560,"children":2561},{},[2562],{"type":444,"value":2563},"Gene expression rank from all samples.",{"type":429,"tag":495,"props":2565,"children":2566},{},[2567],{"type":444,"value":2568},"Joining of SV breakpoint 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",{"type":429,"tag":476,"props":8071,"children":8074},{"href":8072,"rel":8073},"https://www.dnanexus.com/",[480],[8075],{"type":444,"value":8072},{"type":444,"value":484},{"type":429,"tag":436,"props":8078,"children":8079},{},[8080],{"type":444,"value":8081},"Next, store your track files on the platform by uploading them to a \"project folder\".",{"type":429,"tag":436,"props":8083,"children":8084},{},[8085],{"type":444,"value":8086},"For example, following files \"TCGA_DLBC.*\" have been stored in the folder.",{"type":429,"tag":436,"props":8088,"children":8089},{},[8090],{"type":429,"tag":514,"props":8091,"children":8094},{"alt":8092,"src":8093},"img 62","/img/visualization-community/genomepaint/genomepaint-user-guide/image62.png",[],{"type":429,"tag":436,"props":8096,"children":8097},{},[8098,8100,8105],{"type":444,"value":8099},"Follow the instructions in the next section to obtain the ",{"type":429,"tag":440,"props":8101,"children":8102},{},[8103],{"type":444,"value":8104},"GenomePaint FileViewer",{"type":444,"value":484},{"type":429,"tag":436,"props":8107,"children":8108},{},[8109],{"type":444,"value":8110},"Once obtained, the FileViewer looks like below in your account.",{"type":429,"tag":436,"props":8112,"children":8113},{},[8114],{"type":429,"tag":514,"props":8115,"children":8118},{"alt":8116,"src":8117},"img 77","/img/visualization-community/genomepaint/genomepaint-user-guide/image77.png",[],{"type":429,"tag":436,"props":8120,"children":8121},{},[8122],{"type":444,"value":8123},"Click the FileViewer to open up the file selection interface.",{"type":429,"tag":436,"props":8125,"children":8126},{},[8127],{"type":429,"tag":514,"props":8128,"children":8131},{"alt":8129,"src":8130},"img 93","/img/visualization-community/genomepaint/genomepaint-user-guide/image93.png",[],{"type":429,"tag":436,"props":8133,"children":8134},{},[8135],{"type":444,"value":8136},"Select the necessary track files.",{"type":429,"tag":436,"props":8138,"children":8139},{},[8140],{"type":429,"tag":514,"props":8141,"children":8144},{"alt":8142,"src":8143},"img 92","/img/visualization-community/genomepaint/genomepaint-user-guide/image92.png",[],{"type":429,"tag":436,"props":8146,"children":8147},{},[8148],{"type":444,"value":8149},"Click the button \"Launch viewer\" at bottom right.\nThe Viewer will start up by prompting you to select the correct genome build for your data.",{"type":429,"tag":436,"props":8151,"children":8152},{},[8153],{"type":429,"tag":514,"props":8154,"children":8157},{"alt":8155,"src":8156},"img 21","/img/visualization-community/genomepaint/genomepaint-user-guide/image21.png",[],{"type":429,"tag":436,"props":8159,"children":8160},{},[8161],{"type":444,"value":8162},"By selecting a genome build, GenomePaint will launch and show your custom track.",{"type":429,"tag":464,"props":8164,"children":8166},{"id":8165},"obtaining-the-genomepaint-fileviewer-on-dnanexus",[8167],{"type":444,"value":8168},"Obtaining the GenomePaint FileViewer on DNAnexus",{"type":429,"tag":436,"props":8170,"children":8171},{},[8172,8174,8180],{"type":444,"value":8173},"Install the \"dx-toolkit\" on your computer by following instructions on ",{"type":429,"tag":476,"props":8175,"children":8178},{"href":8176,"rel":8177},"https://documentation.dnanexus.com/downloads",[480],[8179],{"type":444,"value":8176},{"type":444,"value":484},{"type":429,"tag":436,"props":8182,"children":8183},{},[8184],{"type":444,"value":8185},"Once installed, you will be able to run the \"dx\" command on your computer.",{"type":429,"tag":436,"props":8187,"children":8188},{},[8189,8191,8197],{"type":444,"value":8190},"Next, login at the dx-toolkit with your token.\nTo obtain a token, at a web browser, log yourself in at ",{"type":429,"tag":476,"props":8192,"children":8195},{"href":8193,"rel":8194},"https://platform.dnanexus.com/",[480],[8196],{"type":444,"value":8193},{"type":444,"value":8198},".\nClick the top-right user icon and select \"My Profile\".",{"type":429,"tag":436,"props":8200,"children":8201},{},[8202],{"type":429,"tag":514,"props":8203,"children":8206},{"alt":8204,"src":8205},"img 81","/img/visualization-community/genomepaint/genomepaint-user-guide/image81.png",[],{"type":429,"tag":436,"props":8208,"children":8209},{},[8210],{"type":444,"value":8211},"Then, click the \"API Tokens\" tab.\nThen click the \"+ New Token\" button.",{"type":429,"tag":436,"props":8213,"children":8214},{},[8215],{"type":429,"tag":514,"props":8216,"children":8219},{"alt":8217,"src":8218},"img 24","/img/visualization-community/genomepaint/genomepaint-user-guide/image24.png",[],{"type":429,"tag":436,"props":8221,"children":8222},{},[8223],{"type":444,"value":8224},"At the prompt, enter a label and click \"Generate Token\".",{"type":429,"tag":436,"props":8226,"children":8227},{},[8228],{"type":429,"tag":514,"props":8229,"children":8232},{"alt":8230,"src":8231},"img 89","/img/visualization-community/genomepaint/genomepaint-user-guide/image89.png",[],{"type":429,"tag":436,"props":8234,"children":8235},{},[8236],{"type":444,"value":8237},"The token is now displayed.\nSelect and copy it.",{"type":429,"tag":436,"props":8239,"children":8240},{},[8241],{"type":429,"tag":514,"props":8242,"children":8245},{"alt":8243,"src":8244},"img 71","/img/visualization-community/genomepaint/genomepaint-user-guide/image71.png",[],{"type":429,"tag":436,"props":8247,"children":8248},{},[8249],{"type":444,"value":8250},"At the terminal of your computer, log into \"dx\" with the token.",{"type":429,"tag":1738,"props":8252,"children":8254},{"className":2791,"code":8253,"language":2793,"meta":424,"style":424},"dx login --token TvmrnvgkHeyYouCanChargeYourElectricCarForFreeAtWork\n\n# Available projects (CONTRIBUTE or higher):\n# … here lists your projects … \n\n# Pick a numbered choice:\n",[8255],{"type":429,"tag":1744,"props":8256,"children":8257},{"__ignoreMap":424},[8258,8281,8288,8297,8305,8312],{"type":429,"tag":1748,"props":8259,"children":8260},{"class":1750,"line":1751},[8261,8266,8271,8276],{"type":429,"tag":1748,"props":8262,"children":8263},{"style":2803},[8264],{"type":444,"value":8265},"dx",{"type":429,"tag":1748,"props":8267,"children":8268},{"style":2808},[8269],{"type":444,"value":8270}," login",{"type":429,"tag":1748,"props":8272,"children":8273},{"style":2808},[8274],{"type":444,"value":8275}," --token",{"type":429,"tag":1748,"props":8277,"children":8278},{"style":2808},[8279],{"type":444,"value":8280}," TvmrnvgkHeyYouCanChargeYourElectricCarForFreeAtWork\n",{"type":429,"tag":1748,"props":8282,"children":8283},{"class":1750,"line":1760},[8284],{"type":429,"tag":1748,"props":8285,"children":8286},{"emptyLinePlaceholder":7099},[8287],{"type":444,"value":7102},{"type":429,"tag":1748,"props":8289,"children":8290},{"class":1750,"line":1769},[8291],{"type":429,"tag":1748,"props":8292,"children":8294},{"style":8293},"--shiki-light:#90A4AE;--shiki-light-font-style:italic;--shiki-default:#546E7A;--shiki-default-font-style:italic;--shiki-dark:#676E95;--shiki-dark-font-style:italic",[8295],{"type":444,"value":8296},"# Available projects (CONTRIBUTE or higher):\n",{"type":429,"tag":1748,"props":8298,"children":8299},{"class":1750,"line":1778},[8300],{"type":429,"tag":1748,"props":8301,"children":8302},{"style":8293},[8303],{"type":444,"value":8304},"# … here lists your projects … \n",{"type":429,"tag":1748,"props":8306,"children":8307},{"class":1750,"line":1787},[8308],{"type":429,"tag":1748,"props":8309,"children":8310},{"emptyLinePlaceholder":7099},[8311],{"type":444,"value":7102},{"type":429,"tag":1748,"props":8313,"children":8314},{"class":1750,"line":1796},[8315],{"type":429,"tag":1748,"props":8316,"children":8317},{"style":8293},[8318],{"type":444,"value":8319},"# Pick a numbered choice:\n",{"type":429,"tag":436,"props":8321,"children":8322},{},[8323,8325,8331],{"type":444,"value":8324},"Enter a number to select a project.\nYou are now logged into your account.\nRun ",{"type":429,"tag":1744,"props":8326,"children":8328},{"className":8327},[],[8329],{"type":444,"value":8330},"dx ls",{"type":444,"value":8332}," to do a directory listing on the selected project.\nNext, upload the GenomePaint FileViewer to this project.",{"type":429,"tag":436,"props":8334,"children":8335},{},[8336],{"type":444,"value":8337},"Run this command to download the FileViewer source code, to a file named \"GenomePaint (SVCNV, VCF, FPKM)\".",{"type":429,"tag":1738,"props":8339,"children":8341},{"className":2791,"code":8340,"language":2793,"meta":424,"style":424},"wget 'https://pecan.stjude.cloud/static/fileviewers/GenomePaint%20(SVCNV%2C%20VCF%2C%20FPKM)'\n",[8342],{"type":429,"tag":1744,"props":8343,"children":8344},{"__ignoreMap":424},[8345],{"type":429,"tag":1748,"props":8346,"children":8347},{"class":1750,"line":1751},[8348,8353,8358,8363],{"type":429,"tag":1748,"props":8349,"children":8350},{"style":2803},[8351],{"type":444,"value":8352},"wget",{"type":429,"tag":1748,"props":8354,"children":8355},{"style":2919},[8356],{"type":444,"value":8357}," '",{"type":429,"tag":1748,"props":8359,"children":8360},{"style":2808},[8361],{"type":444,"value":8362},"https://pecan.stjude.cloud/static/fileviewers/GenomePaint%20(SVCNV%2C%20VCF%2C%20FPKM)",{"type":429,"tag":1748,"props":8364,"children":8365},{"style":2919},[8366],{"type":444,"value":7619},{"type":429,"tag":436,"props":8368,"children":8369},{},[8370],{"type":444,"value":8371},"Run this command to upload the file to your DNAnexus project as a FileViewer.",{"type":429,"tag":1738,"props":8373,"children":8375},{"className":2791,"code":8374,"language":2793,"meta":424,"style":424},"dx upload --type FileViewer 'GenomePaint (SVCNV, VCF, FPKM)' \n# [===========================================================>] Uploaded 5,257 of 5,257 bytes (100%) /.../GenomePaint (SVCNV, VCF, FPKM)\n# ID                  file-Fjypgf...\n# Class               file\n# Project             project-F0QQBv...\n# Folder              /\n# Name                GenomePaint (SVCNV, VCF, FPKM)\n# State               closing\n# Visibility          visible\n# Types               FileViewer\n# Properties          -\n# Tags                -\n# Outgoing links      -\n# Created             Fri Feb  7 12:26:32 2020\n# Created by          xzhou\n# Last modified       Fri Feb  7 12:26:33 2020\n# archivalState       \"live\"\n# Media type\n",[8376],{"type":429,"tag":1744,"props":8377,"children":8378},{"__ignoreMap":424},[8379,8419,8427,8435,8443,8451,8459,8467,8475,8483,8491,8499,8507,8515,8523,8531,8539,8547],{"type":429,"tag":1748,"props":8380,"children":8381},{"class":1750,"line":1751},[8382,8386,8391,8396,8401,8405,8410,8414],{"type":429,"tag":1748,"props":8383,"children":8384},{"style":2803},[8385],{"type":444,"value":8265},{"type":429,"tag":1748,"props":8387,"children":8388},{"style":2808},[8389],{"type":444,"value":8390}," upload",{"type":429,"tag":1748,"props":8392,"children":8393},{"style":2808},[8394],{"type":444,"value":8395}," --type",{"type":429,"tag":1748,"props":8397,"children":8398},{"style":2808},[8399],{"type":444,"value":8400}," FileViewer",{"type":429,"tag":1748,"props":8402,"children":8403},{"style":2919},[8404],{"type":444,"value":8357},{"type":429,"tag":1748,"props":8406,"children":8407},{"style":2808},[8408],{"type":444,"value":8409},"GenomePaint (SVCNV, VCF, FPKM)",{"type":429,"tag":1748,"props":8411,"children":8412},{"style":2919},[8413],{"type":444,"value":7293},{"type":429,"tag":1748,"props":8415,"children":8416},{"style":3002},[8417],{"type":444,"value":8418}," \n",{"type":429,"tag":1748,"props":8420,"children":8421},{"class":1750,"line":1760},[8422],{"type":429,"tag":1748,"props":8423,"children":8424},{"style":8293},[8425],{"type":444,"value":8426},"# [===========================================================>] Uploaded 5,257 of 5,257 bytes (100%) /.../GenomePaint (SVCNV, VCF, FPKM)\n",{"type":429,"tag":1748,"props":8428,"children":8429},{"class":1750,"line":1769},[8430],{"type":429,"tag":1748,"props":8431,"children":8432},{"style":8293},[8433],{"type":444,"value":8434},"# ID                  file-Fjypgf...\n",{"type":429,"tag":1748,"props":8436,"children":8437},{"class":1750,"line":1778},[8438],{"type":429,"tag":1748,"props":8439,"children":8440},{"style":8293},[8441],{"type":444,"value":8442},"# Class               file\n",{"type":429,"tag":1748,"props":8444,"children":8445},{"class":1750,"line":1787},[8446],{"type":429,"tag":1748,"props":8447,"children":8448},{"style":8293},[8449],{"type":444,"value":8450},"# Project             project-F0QQBv...\n",{"type":429,"tag":1748,"props":8452,"children":8453},{"class":1750,"line":1796},[8454],{"type":429,"tag":1748,"props":8455,"children":8456},{"style":8293},[8457],{"type":444,"value":8458},"# Folder              /\n",{"type":429,"tag":1748,"props":8460,"children":8461},{"class":1750,"line":1805},[8462],{"type":429,"tag":1748,"props":8463,"children":8464},{"style":8293},[8465],{"type":444,"value":8466},"# Name                GenomePaint (SVCNV, VCF, FPKM)\n",{"type":429,"tag":1748,"props":8468,"children":8469},{"class":1750,"line":1814},[8470],{"type":429,"tag":1748,"props":8471,"children":8472},{"style":8293},[8473],{"type":444,"value":8474},"# State               closing\n",{"type":429,"tag":1748,"props":8476,"children":8477},{"class":1750,"line":1823},[8478],{"type":429,"tag":1748,"props":8479,"children":8480},{"style":8293},[8481],{"type":444,"value":8482},"# Visibility          visible\n",{"type":429,"tag":1748,"props":8484,"children":8485},{"class":1750,"line":1832},[8486],{"type":429,"tag":1748,"props":8487,"children":8488},{"style":8293},[8489],{"type":444,"value":8490},"# Types               FileViewer\n",{"type":429,"tag":1748,"props":8492,"children":8493},{"class":1750,"line":1841},[8494],{"type":429,"tag":1748,"props":8495,"children":8496},{"style":8293},[8497],{"type":444,"value":8498},"# Properties          -\n",{"type":429,"tag":1748,"props":8500,"children":8501},{"class":1750,"line":1850},[8502],{"type":429,"tag":1748,"props":8503,"children":8504},{"style":8293},[8505],{"type":444,"value":8506},"# Tags                -\n",{"type":429,"tag":1748,"props":8508,"children":8509},{"class":1750,"line":1859},[8510],{"type":429,"tag":1748,"props":8511,"children":8512},{"style":8293},[8513],{"type":444,"value":8514},"# Outgoing links      -\n",{"type":429,"tag":1748,"props":8516,"children":8517},{"class":1750,"line":1868},[8518],{"type":429,"tag":1748,"props":8519,"children":8520},{"style":8293},[8521],{"type":444,"value":8522},"# Created             Fri Feb  7 12:26:32 2020\n",{"type":429,"tag":1748,"props":8524,"children":8525},{"class":1750,"line":1877},[8526],{"type":429,"tag":1748,"props":8527,"children":8528},{"style":8293},[8529],{"type":444,"value":8530},"# Created by          xzhou\n",{"type":429,"tag":1748,"props":8532,"children":8533},{"class":1750,"line":1886},[8534],{"type":429,"tag":1748,"props":8535,"children":8536},{"style":8293},[8537],{"type":444,"value":8538},"# Last modified       Fri Feb  7 12:26:33 2020\n",{"type":429,"tag":1748,"props":8540,"children":8541},{"class":1750,"line":1895},[8542],{"type":429,"tag":1748,"props":8543,"children":8544},{"style":8293},[8545],{"type":444,"value":8546},"# archivalState       \"live\"\n",{"type":429,"tag":1748,"props":8548,"children":8549},{"class":1750,"line":1904},[8550],{"type":429,"tag":1748,"props":8551,"children":8552},{"style":8293},[8553],{"type":444,"value":8554},"# Media type\n",{"type":429,"tag":436,"props":8556,"children":8557},{},[8558],{"type":444,"value":8559},"With this, you have successfully obtained the GenomePaint FileViewer on your DNAnexus account.",{"type":429,"tag":464,"props":8561,"children":8563},{"id":8562},"hosting-and-launching-custom-genomepaint-track-from-amazon-aws",[8564],{"type":444,"value":8565},"Hosting and launching custom GenomePaint track from Amazon AWS",{"type":429,"tag":774,"props":8567,"children":8569},{"id":8568},"amazon-s3-introduction",[8570],{"type":444,"value":8571},"Amazon S3 Introduction",{"type":429,"tag":436,"props":8573,"children":8574},{},[8575,8577,8584],{"type":444,"value":8576},"Amazon AWS has secure and highly available storage service known as S3.\nAmazon S3 stores data as objects within buckets.\nAn object consists of a file and optional metadata.\nTo store an object in Amazon S3, you upload a file to a bucket.\nWhen uploading, you can set permissions on the object and any metadata.\nLikewise many settings can be configured for a bucket.\nTo get familiarized with common terminologies used for Amazon S3, ",{"type":429,"tag":476,"props":8578,"children":8581},{"href":8579,"rel":8580},"https://docs.aws.amazon.com/AmazonS3/latest/gsg/AmazonS3Basics.html",[480],[8582],{"type":444,"value":8583},"checkout the official guide",{"type":444,"value":484},{"type":429,"tag":774,"props":8586,"children":8588},{"id":8587},"sign-up-for-amazon-s3",[8589],{"type":444,"value":8590},"Sign Up for Amazon S3",{"type":429,"tag":436,"props":8592,"children":8593},{},[8594,8596,8602],{"type":444,"value":8595},"Go to ",{"type":429,"tag":476,"props":8597,"children":8600},{"href":8598,"rel":8599},"https://aws.amazon.com/s3/",[480],[8601],{"type":444,"value":8598},{"type":444,"value":8603}," and click \"Create an AWS account\".\nOnce created, AWS will notify you by email when your account is active and available for you to use.",{"type":429,"tag":774,"props":8605,"children":8607},{"id":8606},"create-a-new-bucket-on-s3",[8608],{"type":444,"value":8609},"Create a new Bucket on S3",{"type":429,"tag":436,"props":8611,"children":8612},{},[8613,8615,8621],{"type":444,"value":8614},"Login to your account and access the \"S3 Management Console\" at ",{"type":429,"tag":476,"props":8616,"children":8619},{"href":8617,"rel":8618},"https://console.aws.amazon.com/s3/",[480],[8620],{"type":444,"value":8617},{"type":444,"value":8622},".\nHere, click the \"+ Create bucket\" button.",{"type":429,"tag":436,"props":8624,"children":8625},{},[8626],{"type":429,"tag":514,"props":8627,"children":8630},{"alt":8628,"src":8629},"img 40","/img/visualization-community/genomepaint/genomepaint-user-guide/image40.png",[],{"type":429,"tag":436,"props":8632,"children":8633},{},[8634],{"type":444,"value":8635},"A new window pops up with details required for creating a new bucket.",{"type":429,"tag":436,"props":8637,"children":8638},{},[8639],{"type":429,"tag":514,"props":8640,"children":8643},{"alt":8641,"src":8642},"img 27","/img/visualization-community/genomepaint/genomepaint-user-guide/image27.png",[],{"type":429,"tag":436,"props":8645,"children":8646},{},[8647],{"type":444,"value":8648},"In the 'Bucket name' box enter a unique DNS-compliant name.\nThis name should be unique across all buckets on Amazon S3.\nThe URL for the objects inside the bucket will include the bucket name as well.",{"type":429,"tag":436,"props":8650,"children":8651},{},[8652],{"type":444,"value":8653},"At \"Configure options\", you can change the settings or keep default as per requirements.",{"type":429,"tag":436,"props":8655,"children":8656},{},[8657],{"type":444,"value":8658},"At \"Set permissions\", make the bucket public so files can be accessible from GenomePaint.\nTo make the Bucket public, leave all the checkboxes unchecked.",{"type":429,"tag":436,"props":8660,"children":8661},{},[8662],{"type":429,"tag":514,"props":8663,"children":8666},{"alt":8664,"src":8665},"img 79","/img/visualization-community/genomepaint/genomepaint-user-guide/image79.png",[],{"type":429,"tag":436,"props":8668,"children":8669},{},[8670],{"type":444,"value":8671},"Next page will summarize all settings for the new bucket.\nAfter confirming, click \"Create bucket\".",{"type":429,"tag":774,"props":8673,"children":8675},{"id":8674},"add-custom-track-files-to-a-bucket",[8676],{"type":444,"value":8677},"Add custom track files to a Bucket",{"type":429,"tag":436,"props":8679,"children":8680},{},[8681],{"type":444,"value":8682},"Select the bucket you want files to upload to.",{"type":429,"tag":436,"props":8684,"children":8685},{},[8686],{"type":429,"tag":514,"props":8687,"children":8690},{"alt":8688,"src":8689},"img 32","/img/visualization-community/genomepaint/genomepaint-user-guide/image32.png",[],{"type":429,"tag":436,"props":8692,"children":8693},{},[8694],{"type":444,"value":8695},"Then, click the \"Upload\" button.",{"type":429,"tag":436,"props":8697,"children":8698},{},[8699],{"type":429,"tag":514,"props":8700,"children":8703},{"alt":8701,"src":8702},"img 59","/img/visualization-community/genomepaint/genomepaint-user-guide/image59.png",[],{"type":429,"tag":436,"props":8705,"children":8706},{},[8707],{"type":444,"value":8708},"On the next page, select all the GenomePaint track files and associated index files for uploading.",{"type":429,"tag":436,"props":8710,"children":8711},{},[8712],{"type":429,"tag":514,"props":8713,"children":8716},{"alt":8714,"src":8715},"img 80","/img/visualization-community/genomepaint/genomepaint-user-guide/image80.png",[],{"type":429,"tag":436,"props":8718,"children":8719},{},[8720],{"type":444,"value":8721},"Once a file is selected, it will appear in the menu.\nClick 'Upload' at the bottom.\nMake sure to add index files (.tbi and .csi) with the vcf, svcnv or fpkm files.",{"type":429,"tag":436,"props":8723,"children":8724},{},[8725],{"type":429,"tag":514,"props":8726,"children":8729},{"alt":8727,"src":8728},"img 35","/img/visualization-community/genomepaint/genomepaint-user-guide/image35.png",[],{"type":429,"tag":774,"props":8731,"children":8733},{"id":8732},"enable-public-access-to-the-track-files",[8734],{"type":444,"value":8735},"Enable public access to the track files",{"type":429,"tag":436,"props":8737,"children":8738},{},[8739],{"type":444,"value":8740},"Once the file is uploaded to the bucket, it will appear in the list of files.",{"type":429,"tag":436,"props":8742,"children":8743},{},[8744],{"type":429,"tag":514,"props":8745,"children":8748},{"alt":8746,"src":8747},"img 7","/img/visualization-community/genomepaint/genomepaint-user-guide/image7.png",[],{"type":429,"tag":436,"props":8750,"children":8751},{},[8752],{"type":444,"value":8753},"Select all the files you want to visualize in the GenomePaint.\nClick \"Actions\" and select \"Make 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