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Merge branch 'unstable'
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@msalihaltun
msalihaltun committed Feb 10, 2021
2 parents f76d5c9 + 4683c04 commit 1f57b94
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4 changes: 2 additions & 2 deletions dist/index.html
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<!-- TODO this is a quick fix for the excluded 3rd party css dependencies, it is probably not a good idea to have direct references to github cdn -->
<link rel="stylesheet" href="https://cdn.rawgit.com/cytoscape/cytoscape.js-panzoom/master/cytoscape.js-panzoom.css">
<link rel="stylesheet" href="https://cdn.rawgit.com/cytoscape/cytoscape.js-navigator/master/cytoscape.js-navigator.css">
<link href="./base.css?aaebb1fcad1d0ba83c93" rel="stylesheet"></head>
<link href="./base.css?ae81cc6bff8b8f929a0e" rel="stylesheet"></head>

<body class="pathwayMapper">
<div>
<div id="app"></div>
</div>
<script type="text/javascript" src="react-pathway-mapper.es5.js?aaebb1fcad1d0ba83c93"></script></body>
<script type="text/javascript" src="react-pathway-mapper.es5.js?ae81cc6bff8b8f929a0e"></script></body>

</html>
23 changes: 21 additions & 2 deletions dist/react-pathway-mapper.es5.js
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2 changes: 1 addition & 1 deletion dist/react-pathway-mapper.es5.js.map
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2 changes: 1 addition & 1 deletion dist/ui/Ranking.d.ts
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Expand Up @@ -18,7 +18,7 @@ export default class Ranking extends React.Component<IRankingProps, {}> {
isExpanded: boolean;
readonly COUNT_PERC_EXPLANATION = "Whether we should favor the number of genes of interest matching the ones in a pathway or the percentage of such genes in that pathway. For instance, suppose genes of interest are A, B, and C, and the pathway contains genes B, C, D, and E. When we consider count, the score is 2 (for the two genes that match). However, when we consider percentage the score will be 50% as 2 of the 4 genes in the pathway are among genes of interest.";
readonly ALTERATION_EXPLANATION = "When this is checked, each matching gene will not directly contribute to the score as 1 unit but with the alteration frequency percentage of that gene. For instance, suppose genes of interest are A, B, and C with alteration frequencies of 0.5, 0.2, and 0.3, respectively, and the pathway contains genes B, C, D, and E. When this is option isn't checked, the score will be 2 for match count and 50% for the match percentage. However, when this option is checked, the scores will be 0.2+0.3=0.5 and (0.2+0.3)/4=12.5% for match count and percentage, respectively.";
readonly TCGA_PANCAN_EXPLANATION = "The pathways listed above were retrieved from PathwayMapper. When this option is checked, only the pathways under TCGA > PanCanAtlas will be shown. Uncheck to show all.";
readonly TCGA_PANCAN_EXPLANATION = "The pathways listed above were retrieved from <a href='http://www.pathwaymapper.org' target='_blank'>PathwayMapper</a>. When this option is checked, only the pathways under TCGA > PanCanAtlas will be shown. Uncheck to show all.";
constructor(props: IRankingProps);
setBestPathwayMethod(i: number): void;
onPathwayClick(pathway: string): void;
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1 change: 1 addition & 0 deletions dist/ui/react-pathway-mapper.d.ts
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Expand Up @@ -131,6 +131,7 @@ export default class PathwayMapper extends React.Component<IPathwayMapperProps,
emphasizeQueryGenes(): void;
render(): JSX.Element;
componentDidMount(): void;
componentDidUpdate(): void;
handleOpen(modalId: EModalType): void;
handleClose(modalId: EModalType): void;
editorHandler(editor: any, eh: any, undoRedoManager: any): void;
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85 changes: 51 additions & 34 deletions samples/HIPPO.txt
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@@ -1,38 +1,55 @@
HIPPO
HIPPO

Involved in the control of organ size. Central to this pathway is the regulation of the transcription co-activators YAP/TAZ that promote the transcription of genes involved in cell proliferation.

--NODE_NAME NODE_ID NODE_TYPE PARENT_ID POSX POSY--
HRAS 7o723KjtxLw3 GENE m8n8vtNexLwr 322 183
NF1 CoRREfZLxLxE GENE -1 399 270
Survival PwPgvbNpxLvq PROCESS -1 791 584
RAS zoIJL9SXxLvs FAMILY -1 505 98
FGFR3 xdJHuZOJxLvx GENE zoIJL9SXxLvs 272 98
ERBB2 2TufgUnDxLvu GENE zoIJL9SXxLvs 584 98
TSC2 PrCzkSRAxLwV GENE NIuPl9Z4xLwO 503 496
PTEN sYk-4hLPxLvn GENE -1 860 184
STK11 lFDvCMmBxLv9 GENE -1 317 469
INPP4B GLEvKwzFxLwB GENE -1 804 266
MTOR ICScCD_7xLwH GENE -1 722 470
Proliferation uwFqE9I9xLwk PROCESS -1 665 584
RAS m8n8vtNexLwr FAMILY -1 399 183
NRAS gJxmCdGKxLwx GENE m8n8vtNexLwr 476 183
ERBB3 MzpcdmxYxLv6 GENE zoIJL9SXxLvs 739 98
TSC1 RWyL5pe9xLwd GENE NIuPl9Z4xLwO 503 444
TSC NIuPl9Z4xLwO FAMILY -1 503 470
PIK3CA iq8nE1OMxLvj GENE -1 658 184
AKT TiUbnalZxLw_ GENE -1 659 349
EGFR 5XuhH2Y3xLv2 GENE zoIJL9SXxLvs 429 98
--NODE_NAME NODE_ID NODE_TYPE PARENT_ID POSX POSY WIDTH HEIGHT--
8f940396-e035-4b9e-8574-b5eadf26e98c FAMILY -1 91 64 150 52
DCHS1 8d4d3dca-9217-4539-b15e-63ce7f5df09a GENE 8f940396-e035-4b9e-8574-b5eadf26e98c 91 34 150 52
DCHS2 f51ccf81-94a8-425f-80ce-4d55489b9660 GENE 8f940396-e035-4b9e-8574-b5eadf26e98c 91 95 150 52
623300c3-2a9c-45d4-be51-ad67eea733b7 FAMILY -1 369 61 150 52
FAT1 901800a8-6c9f-42f6-a9b6-2e8b1483ec63 GENE 623300c3-2a9c-45d4-be51-ad67eea733b7 291 32 150 52
FAT2 775d810d-bfc1-434c-949d-71f4bd38d374 GENE 623300c3-2a9c-45d4-be51-ad67eea733b7 448 31 150 52
FAT3 c4f71e12-c88e-409d-9f26-7bc84b3f6cb8 GENE 623300c3-2a9c-45d4-be51-ad67eea733b7 291 92 150 52
FAT4 075bc3e3-74b9-4d0c-a20d-58b77cb3c3f6 GENE 623300c3-2a9c-45d4-be51-ad67eea733b7 448 91 150 52
de4dab24-648f-4406-8adf-0c08d62b3173 FAMILY -1 714 60 150 52
TAOK1 3e53e820-8a91-4329-86f1-e59948a9003a GENE de4dab24-648f-4406-8adf-0c08d62b3173 636 32 150 52
TAOK3 7a7b38dc-e47d-4f33-9cec-3570a23b2f85 GENE de4dab24-648f-4406-8adf-0c08d62b3173 636 89 150 52
TAOK2 8a51ead1-a5d3-41b8-bf2e-99fc2169857b GENE de4dab24-648f-4406-8adf-0c08d62b3173 793 31 150 52
a495c90c-7f17-4369-81bc-bc8894ba1c0d FAMILY -1 374 324 456.5888856128265 242.9161558761191
SAV1 267c0160-0919-403d-bd52-ea84c001f357 GENE a495c90c-7f17-4369-81bc-bc8894ba1c0d 277 257 150 52
71e2f614-626b-4fbe-9e18-17c83c401062 FAMILY a495c90c-7f17-4369-81bc-bc8894ba1c0d 455 258 212.8900278180157 116.0130640290517
STK3 9f5e8c36-52a9-4e62-bf7c-b1f3b02d8740 GENE 71e2f614-626b-4fbe-9e18-17c83c401062 455 230 150 52
STK4 3e08fb0d-ef9f-49b9-8037-ed940df282af GENE 71e2f614-626b-4fbe-9e18-17c83c401062 455 287 150 52
7ef3236d-1aa7-4082-a396-751554a11282 FAMILY a495c90c-7f17-4369-81bc-bc8894ba1c0d 277 390 154.12303621103598 117.89002781801568
LATS1 2897d4be-7047-4af4-958b-b978a0d944f5 GENE 7ef3236d-1aa7-4082-a396-751554a11282 277 362 150 52
LATS2 944868e7-e040-49a8-8773-3da725d368c3 GENE 7ef3236d-1aa7-4082-a396-751554a11282 277 419 150 52
b6626b2a-d8ef-4d7a-9645-8e9a7a538795 FAMILY a495c90c-7f17-4369-81bc-bc8894ba1c0d 455 390 150 52
MOB1A 54416ef1-d8c0-492d-b465-49adb95ad62e GENE b6626b2a-d8ef-4d7a-9645-8e9a7a538795 454 362 150 52
MOB1B 44429ea1-e73d-43f8-8caf-c7fb319956ff GENE b6626b2a-d8ef-4d7a-9645-8e9a7a538795 455 419 150 52
4df2d8ec-903b-4445-a7a5-f5b105fd49f1 FAMILY -1 710 324 150 52
NF2 fd29bca1-db7d-4f62-bce0-49510642adb3 GENE 4df2d8ec-903b-4445-a7a5-f5b105fd49f1 709 295 150 52
WWC1 e9119bdc-4312-40a5-837e-dc079d103e63 GENE 4df2d8ec-903b-4445-a7a5-f5b105fd49f1 710 353 150 52
8d5398c4-941f-4153-a392-ebaef3fff177 FAMILY -1 373 590 179.71700255004964 76.76416879170804
YAP1 3cf01f62-ef45-4722-8cad-565456928871 GENE 8d5398c4-941f-4153-a392-ebaef3fff177 373 559 150 52
TAZ 9ed35563-0451-451b-a750-c33f5e94108f GENE 8d5398c4-941f-4153-a392-ebaef3fff177 373 620 150 52
bb742872-aa08-4e50-87de-846f64cea394 FAMILY -1 91 590 150 52
CRB1 1ea26f01-462c-4a16-b568-b9de2242fa5b GENE bb742872-aa08-4e50-87de-846f64cea394 91 560 150 52
CRB2 e054585c-47a2-4b4a-9cb7-cbbfc61e900f GENE bb742872-aa08-4e50-87de-846f64cea394 91 620 150 52
PTPN14 d88a9331-971e-4ad2-817a-a3dadbebd4de GENE -1 606 538 150 52
8f2ee28b-9fc4-4b61-ad07-e0c0b0b4c566 FAMILY -1 606 672 150 52
CSNK1E 63916e9d-dcd6-45db-8fbe-3d480ef92c5f GENE 8f2ee28b-9fc4-4b61-ad07-e0c0b0b4c566 606 640 150 52
CSNK1D 0e5136c0-186c-4aba-893c-7f0ce5bdf56d GENE 8f2ee28b-9fc4-4b61-ad07-e0c0b0b4c566 606 705 150 52
TEAD2 0d1f1291-ec19-4f6d-8e74-1f11a020144b GENE -1 373 794 150 52
Cell proliferation and differentiation fb37aa0c-49bb-4db6-b185-bc5a64a72540 PROCESS -1 372 922 150 52

--EDGE_ID SOURCE TARGET EDGE_TYPEINTERACTION_PUBMED_ID
sFy4CeNZxLxT sYk-4hLPxLvn iq8nE1OMxLvj INHIBITS
YpeP_yDkxLxQ TiUbnalZxLw_ NIuPl9Z4xLwO INHIBITS
t2QHaOQlxLxX NIuPl9Z4xLwO ICScCD_7xLwH INHIBITS
--0Bl7NmxLxb m8n8vtNexLwr iq8nE1OMxLvj ACTIVATES
TihuxwDexLxR GLEvKwzFxLwB iq8nE1OMxLvj INHIBITS
M4uM8zkMxLxZ lFDvCMmBxLv9 NIuPl9Z4xLwO ACTIVATES
JGhy8m8UxLxN zoIJL9SXxLvs m8n8vtNexLwr ACTIVATES
rQyUZobSxLxf ICScCD_7xLwH uwFqE9I9xLwk ACTIVATES
t_83aGiOxLxc ICScCD_7xLwH PwPgvbNpxLvq ACTIVATES
1Jm9fDfkxLxV iq8nE1OMxLvj TiUbnalZxLw_ ACTIVATES
J7C0UYeQxLxK CoRREfZLxLxE m8n8vtNexLwr INHIBITS
--EDGE_ID SOURCE TARGET EDGE_TYPE INTERACTION_PUBMED_ID EDGE_NAME EDGE_BENDS
17a941fe-ab44-43f4-8a4e-daa3939947a1 8f940396-e035-4b9e-8574-b5eadf26e98c a495c90c-7f17-4369-81bc-bc8894ba1c0d ACTIVATES
a7d8a94f-4d02-46ed-8726-9c4e3e8bda7e 623300c3-2a9c-45d4-be51-ad67eea733b7 a495c90c-7f17-4369-81bc-bc8894ba1c0d ACTIVATES
ee173361-b9ad-458a-80d3-0138572470d4 de4dab24-648f-4406-8adf-0c08d62b3173 a495c90c-7f17-4369-81bc-bc8894ba1c0d ACTIVATES
e63e86f3-3b5e-4e37-8837-43d92a67ea7d 4df2d8ec-903b-4445-a7a5-f5b105fd49f1 a495c90c-7f17-4369-81bc-bc8894ba1c0d ACTIVATES
04ca3e1e-1693-4ec6-ab80-2724e2e3a0b9 a495c90c-7f17-4369-81bc-bc8894ba1c0d 8d5398c4-941f-4153-a392-ebaef3fff177 INHIBITS
81a3fb4e-3e69-47b6-b499-e9fdfe65a37e bb742872-aa08-4e50-87de-846f64cea394 8d5398c4-941f-4153-a392-ebaef3fff177 INHIBITS
b6c3a4db-545a-4c25-bf4a-f0a3a8de36d2 8f2ee28b-9fc4-4b61-ad07-e0c0b0b4c566 8d5398c4-941f-4153-a392-ebaef3fff177 INHIBITS
fce1ac6e-bc2e-4369-ab6e-287731618cc1 d88a9331-971e-4ad2-817a-a3dadbebd4de 8d5398c4-941f-4153-a392-ebaef3fff177 INHIBITS
b3fafa92-cfc7-460d-94d1-09ce977c3111 8d5398c4-941f-4153-a392-ebaef3fff177 0d1f1291-ec19-4f6d-8e74-1f11a020144b ACTIVATES
7b0d95b6-acc4-46a0-85e4-9cbacd5b11de 0d1f1291-ec19-4f6d-8e74-1f11a020144b fb37aa0c-49bb-4db6-b185-bc5a64a72540 ACTIVATES
85 changes: 51 additions & 34 deletions src/data/pathways.json
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Expand Up @@ -641,40 +641,57 @@
"",
"Involved in the control of organ size. Central to this pathway is the regulation of the transcription co-activators YAP/TAZ that promote the transcription of genes involved in cell proliferation.",
"",
"--NODE_NAME\tNODE_ID\tNODE_TYPE\tPARENT_ID\tPOSX\tPOSY--",
"HRAS\t7o723KjtxLw3\tGENE\tm8n8vtNexLwr\t322\t183",
"NF1\tCoRREfZLxLxE\tGENE\t-1\t399\t270",
"Survival\tPwPgvbNpxLvq\tPROCESS\t-1\t791\t584",
"RAS\tzoIJL9SXxLvs\tFAMILY\t-1\t505\t98",
"FGFR3\txdJHuZOJxLvx\tGENE\tzoIJL9SXxLvs\t272\t98",
"ERBB2\t2TufgUnDxLvu\tGENE\tzoIJL9SXxLvs\t584\t98",
"TSC2\tPrCzkSRAxLwV\tGENE\tNIuPl9Z4xLwO\t503\t496",
"PTEN\tsYk-4hLPxLvn\tGENE\t-1\t860\t184",
"STK11\tlFDvCMmBxLv9\tGENE\t-1\t317\t469",
"INPP4B\tGLEvKwzFxLwB\tGENE\t-1\t804\t266",
"MTOR\tICScCD_7xLwH\tGENE\t-1\t722\t470",
"Proliferation\tuwFqE9I9xLwk\tPROCESS\t-1\t665\t584",
"RAS\tm8n8vtNexLwr\tFAMILY\t-1\t399\t183",
"NRAS\tgJxmCdGKxLwx\tGENE\tm8n8vtNexLwr\t476\t183",
"ERBB3\tMzpcdmxYxLv6\tGENE\tzoIJL9SXxLvs\t739\t98",
"TSC1\tRWyL5pe9xLwd\tGENE\tNIuPl9Z4xLwO\t503\t444",
"TSC\tNIuPl9Z4xLwO\tFAMILY\t-1\t503\t470",
"PIK3CA\tiq8nE1OMxLvj\tGENE\t-1\t658\t184",
"AKT\tTiUbnalZxLw_\tGENE\t-1\t659\t349",
"EGFR\t5XuhH2Y3xLv2\tGENE\tzoIJL9SXxLvs\t429\t98",
"",
"--EDGE_ID\tSOURCE\tTARGET\tEDGE_TYPEINTERACTION_PUBMED_ID",
"sFy4CeNZxLxT\tsYk-4hLPxLvn\tiq8nE1OMxLvj\tINHIBITS\t",
"YpeP_yDkxLxQ\tTiUbnalZxLw_\tNIuPl9Z4xLwO\tINHIBITS\t",
"t2QHaOQlxLxX\tNIuPl9Z4xLwO\tICScCD_7xLwH\tINHIBITS\t",
"--0Bl7NmxLxb\tm8n8vtNexLwr\tiq8nE1OMxLvj\tACTIVATES\t",
"TihuxwDexLxR\tGLEvKwzFxLwB\tiq8nE1OMxLvj\tINHIBITS\t",
"M4uM8zkMxLxZ\tlFDvCMmBxLv9\tNIuPl9Z4xLwO\tACTIVATES\t",
"JGhy8m8UxLxN\tzoIJL9SXxLvs\tm8n8vtNexLwr\tACTIVATES\t",
"rQyUZobSxLxf\tICScCD_7xLwH\tuwFqE9I9xLwk\tACTIVATES\t",
"t_83aGiOxLxc\tICScCD_7xLwH\tPwPgvbNpxLvq\tACTIVATES\t",
"1Jm9fDfkxLxV\tiq8nE1OMxLvj\tTiUbnalZxLw_\tACTIVATES\t",
"J7C0UYeQxLxK\tCoRREfZLxLxE\tm8n8vtNexLwr\tINHIBITS\t"
"--NODE_NAME\tNODE_ID\tNODE_TYPE\tPARENT_ID\tPOSX\tPOSY\tWIDTH\tHEIGHT--",
"\t8f940396-e035-4b9e-8574-b5eadf26e98c\tFAMILY\t-1\t91\t64\t150\t52",
"DCHS1\t8d4d3dca-9217-4539-b15e-63ce7f5df09a\tGENE\t8f940396-e035-4b9e-8574-b5eadf26e98c\t91\t34\t150\t52",
"DCHS2\tf51ccf81-94a8-425f-80ce-4d55489b9660\tGENE\t8f940396-e035-4b9e-8574-b5eadf26e98c\t91\t95\t150\t52",
"\t623300c3-2a9c-45d4-be51-ad67eea733b7\tFAMILY\t-1\t369\t61\t150\t52",
"FAT1\t901800a8-6c9f-42f6-a9b6-2e8b1483ec63\tGENE\t623300c3-2a9c-45d4-be51-ad67eea733b7\t291\t32\t150\t52",
"FAT2\t775d810d-bfc1-434c-949d-71f4bd38d374\tGENE\t623300c3-2a9c-45d4-be51-ad67eea733b7\t448\t31\t150\t52",
"FAT3\tc4f71e12-c88e-409d-9f26-7bc84b3f6cb8\tGENE\t623300c3-2a9c-45d4-be51-ad67eea733b7\t291\t92\t150\t52",
"FAT4\t075bc3e3-74b9-4d0c-a20d-58b77cb3c3f6\tGENE\t623300c3-2a9c-45d4-be51-ad67eea733b7\t448\t91\t150\t52",
"\tde4dab24-648f-4406-8adf-0c08d62b3173\tFAMILY\t-1\t714\t60\t150\t52",
"TAOK1\t3e53e820-8a91-4329-86f1-e59948a9003a\tGENE\tde4dab24-648f-4406-8adf-0c08d62b3173\t636\t32\t150\t52",
"TAOK3\t7a7b38dc-e47d-4f33-9cec-3570a23b2f85\tGENE\tde4dab24-648f-4406-8adf-0c08d62b3173\t636\t89\t150\t52",
"TAOK2\t8a51ead1-a5d3-41b8-bf2e-99fc2169857b\tGENE\tde4dab24-648f-4406-8adf-0c08d62b3173\t793\t31\t150\t52",
"\ta495c90c-7f17-4369-81bc-bc8894ba1c0d\tFAMILY\t-1\t374\t324\t456.5888856128265\t242.9161558761191",
"SAV1\t267c0160-0919-403d-bd52-ea84c001f357\tGENE\ta495c90c-7f17-4369-81bc-bc8894ba1c0d\t277\t257\t150\t52",
"\t71e2f614-626b-4fbe-9e18-17c83c401062\tFAMILY\ta495c90c-7f17-4369-81bc-bc8894ba1c0d\t455\t258\t212.8900278180157\t116.0130640290517",
"STK3\t9f5e8c36-52a9-4e62-bf7c-b1f3b02d8740\tGENE\t71e2f614-626b-4fbe-9e18-17c83c401062\t455\t230\t150\t52",
"STK4\t3e08fb0d-ef9f-49b9-8037-ed940df282af\tGENE\t71e2f614-626b-4fbe-9e18-17c83c401062\t455\t287\t150\t52",
"\t7ef3236d-1aa7-4082-a396-751554a11282\tFAMILY\ta495c90c-7f17-4369-81bc-bc8894ba1c0d\t277\t390\t154.12303621103598\t117.89002781801568",
"LATS1\t2897d4be-7047-4af4-958b-b978a0d944f5\tGENE\t7ef3236d-1aa7-4082-a396-751554a11282\t277\t362\t150\t52",
"LATS2\t944868e7-e040-49a8-8773-3da725d368c3\tGENE\t7ef3236d-1aa7-4082-a396-751554a11282\t277\t419\t150\t52",
"\tb6626b2a-d8ef-4d7a-9645-8e9a7a538795\tFAMILY\ta495c90c-7f17-4369-81bc-bc8894ba1c0d\t455\t390\t150\t52",
"MOB1A\t54416ef1-d8c0-492d-b465-49adb95ad62e\tGENE\tb6626b2a-d8ef-4d7a-9645-8e9a7a538795\t454\t362\t150\t52",
"MOB1B\t44429ea1-e73d-43f8-8caf-c7fb319956ff\tGENE\tb6626b2a-d8ef-4d7a-9645-8e9a7a538795\t455\t419\t150\t52",
"\t4df2d8ec-903b-4445-a7a5-f5b105fd49f1\tFAMILY\t-1\t710\t324\t150\t52",
"NF2\tfd29bca1-db7d-4f62-bce0-49510642adb3\tGENE\t4df2d8ec-903b-4445-a7a5-f5b105fd49f1\t709\t295\t150\t52",
"WWC1\te9119bdc-4312-40a5-837e-dc079d103e63\tGENE\t4df2d8ec-903b-4445-a7a5-f5b105fd49f1\t710\t353\t150\t52",
"\t8d5398c4-941f-4153-a392-ebaef3fff177\tFAMILY\t-1\t373\t590\t179.71700255004964\t76.76416879170804",
"YAP1\t3cf01f62-ef45-4722-8cad-565456928871\tGENE\t8d5398c4-941f-4153-a392-ebaef3fff177\t373\t559\t150\t52",
"TAZ\t9ed35563-0451-451b-a750-c33f5e94108f\tGENE\t8d5398c4-941f-4153-a392-ebaef3fff177\t373\t620\t150\t52",
"\tbb742872-aa08-4e50-87de-846f64cea394\tFAMILY\t-1\t91\t590\t150\t52",
"CRB1\t1ea26f01-462c-4a16-b568-b9de2242fa5b\tGENE\tbb742872-aa08-4e50-87de-846f64cea394\t91\t560\t150\t52",
"CRB2\te054585c-47a2-4b4a-9cb7-cbbfc61e900f\tGENE\tbb742872-aa08-4e50-87de-846f64cea394\t91\t620\t150\t52",
"PTPN14\td88a9331-971e-4ad2-817a-a3dadbebd4de\tGENE\t-1\t606\t538\t150\t52",
"\t8f2ee28b-9fc4-4b61-ad07-e0c0b0b4c566\tFAMILY\t-1\t606\t672\t150\t52",
"CSNK1E\t63916e9d-dcd6-45db-8fbe-3d480ef92c5f\tGENE\t8f2ee28b-9fc4-4b61-ad07-e0c0b0b4c566\t606\t640\t150\t52",
"CSNK1D\t0e5136c0-186c-4aba-893c-7f0ce5bdf56d\tGENE\t8f2ee28b-9fc4-4b61-ad07-e0c0b0b4c566\t606\t705\t150\t52",
"TEAD2\t0d1f1291-ec19-4f6d-8e74-1f11a020144b\tGENE\t-1\t373\t794\t150\t52",
"Cell proliferation and differentiation\tfb37aa0c-49bb-4db6-b185-bc5a64a72540\tPROCESS\t-1\t372\t922\t150\t52",
"",
"--EDGE_ID\tSOURCE\tTARGET\tEDGE_TYPE\tINTERACTION_PUBMED_ID\tEDGE_NAME\tEDGE_BENDS",
"17a941fe-ab44-43f4-8a4e-daa3939947a1\t8f940396-e035-4b9e-8574-b5eadf26e98c\ta495c90c-7f17-4369-81bc-bc8894ba1c0d\tACTIVATES\t\t\t",
"a7d8a94f-4d02-46ed-8726-9c4e3e8bda7e\t623300c3-2a9c-45d4-be51-ad67eea733b7\ta495c90c-7f17-4369-81bc-bc8894ba1c0d\tACTIVATES\t\t\t",
"ee173361-b9ad-458a-80d3-0138572470d4\tde4dab24-648f-4406-8adf-0c08d62b3173\ta495c90c-7f17-4369-81bc-bc8894ba1c0d\tACTIVATES\t\t\t",
"e63e86f3-3b5e-4e37-8837-43d92a67ea7d\t4df2d8ec-903b-4445-a7a5-f5b105fd49f1\ta495c90c-7f17-4369-81bc-bc8894ba1c0d\tACTIVATES\t\t\t",
"04ca3e1e-1693-4ec6-ab80-2724e2e3a0b9\ta495c90c-7f17-4369-81bc-bc8894ba1c0d\t8d5398c4-941f-4153-a392-ebaef3fff177\tINHIBITS\t\t\t",
"81a3fb4e-3e69-47b6-b499-e9fdfe65a37e\tbb742872-aa08-4e50-87de-846f64cea394\t8d5398c4-941f-4153-a392-ebaef3fff177\tINHIBITS\t\t\t",
"b6c3a4db-545a-4c25-bf4a-f0a3a8de36d2\t8f2ee28b-9fc4-4b61-ad07-e0c0b0b4c566\t8d5398c4-941f-4153-a392-ebaef3fff177\tINHIBITS\t\t\t",
"fce1ac6e-bc2e-4369-ab6e-287731618cc1\td88a9331-971e-4ad2-817a-a3dadbebd4de\t8d5398c4-941f-4153-a392-ebaef3fff177\tINHIBITS\t\t\t",
"b3fafa92-cfc7-460d-94d1-09ce977c3111\t8d5398c4-941f-4153-a392-ebaef3fff177\t0d1f1291-ec19-4f6d-8e74-1f11a020144b\tACTIVATES\t\t\t",
"7b0d95b6-acc4-46a0-85e4-9cbacd5b11de\t0d1f1291-ec19-4f6d-8e74-1f11a020144b\tfb37aa0c-49bb-4db6-b185-bc5a64a72540\tACTIVATES\t\t\t"
],
"HNSC-2015-Apoptosis-pathway": [
"HNSC-2015-Apoptosis-pathway",
Expand Down
12 changes: 10 additions & 2 deletions src/ui/Ranking.tsx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ export default class Ranking extends React.Component<IRankingProps, {}>{

readonly COUNT_PERC_EXPLANATION = "Whether we should favor the number of genes of interest matching the ones in a pathway or the percentage of such genes in that pathway. For instance, suppose genes of interest are A, B, and C, and the pathway contains genes B, C, D, and E. When we consider count, the score is 2 (for the two genes that match). However, when we consider percentage the score will be 50% as 2 of the 4 genes in the pathway are among genes of interest.";
readonly ALTERATION_EXPLANATION = "When this is checked, each matching gene will not directly contribute to the score as 1 unit but with the alteration frequency percentage of that gene. For instance, suppose genes of interest are A, B, and C with alteration frequencies of 0.5, 0.2, and 0.3, respectively, and the pathway contains genes B, C, D, and E. When this is option isn't checked, the score will be 2 for match count and 50% for the match percentage. However, when this option is checked, the scores will be 0.2+0.3=0.5 and (0.2+0.3)/4=12.5% for match count and percentage, respectively.";
readonly TCGA_PANCAN_EXPLANATION = "The pathways listed above were retrieved from PathwayMapper. When this option is checked, only the pathways under TCGA > PanCanAtlas will be shown. Uncheck to show all.";
readonly TCGA_PANCAN_EXPLANATION = "The pathways listed above were retrieved from <a href='http://www.pathwaymapper.org' target='_blank'>PathwayMapper</a>. When this option is checked, only the pathways under TCGA > PanCanAtlas will be shown. Uncheck to show all.";

constructor(props: IRankingProps){
super(props);
Expand Down Expand Up @@ -140,7 +140,15 @@ export default class Ranking extends React.Component<IRankingProps, {}>{
style={{fontSize: "13px"}}
>
Show TCGA PanCancer Atlas pathways only&nbsp;
<span data-tip={this.TCGA_PANCAN_EXPLANATION} data-border="true" data-type="light" data-place="left" data-effect="solid" className="fa fa-question-circle styles-module__infoIcon__zMiog"></span>
<span data-tip={this.TCGA_PANCAN_EXPLANATION}
data-border="true"
data-type="light"
data-place="left"
data-effect="solid"
data-html="true"
data-delay-hide="500"
className="fa fa-question-circle styles-module__infoIcon__zMiog">
</span>
</Checkbox>
</div>
}
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