{"action":"created","issue":{"url":"https://api.github.com/repos/CBIIT/nci-ctd2-dashboard/issues/54","repository_url":"https://api.github.com/repos/CBIIT/nci-ctd2-dashboard","labels_url":"https://api.github.com/repos/CBIIT/nci-ctd2-dashboard/issues/54/labels{/name}","comments_url":"https://api.github.com/repos/CBIIT/nci-ctd2-dashboard/issues/54/comments","events_url":"https://api.github.com/repos/CBIIT/nci-ctd2-dashboard/issues/54/events","html_url":"https://github.com/CBIIT/nci-ctd2-dashboard/issues/54","id":137613168,"number":54,"title":"some references to mouse genes versus human genes?","user":{"login":"hermidalc","id":461066,"avatar_url":"https://avatars.githubusercontent.com/u/461066?v=3","gravatar_id":"","url":"https://api.github.com/users/hermidalc","html_url":"https://github.com/hermidalc","followers_url":"https://api.github.com/users/hermidalc/followers","following_url":"https://api.github.com/users/hermidalc/following{/other_user}","gists_url":"https://api.github.com/users/hermidalc/gists{/gist_id}","starred_url":"https://api.github.com/users/hermidalc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hermidalc/subscriptions","organizations_url":"https://api.github.com/users/hermidalc/orgs","repos_url":"https://api.github.com/users/hermidalc/repos","events_url":"https://api.github.com/users/hermidalc/events{/privacy}","received_events_url":"https://api.github.com/users/hermidalc/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/CBIIT/nci-ctd2-dashboard/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/CBIIT/nci-ctd2-dashboard/labels/major","name":"major","color":"ededed"}],"state":"closed","locked":false,"assignee":{"login":"n1zea144","id":366003,"avatar_url":"https://avatars.githubusercontent.com/u/366003?v=3","gravatar_id":"","url":"https://api.github.com/users/n1zea144","html_url":"https://github.com/n1zea144","followers_url":"https://api.github.com/users/n1zea144/followers","following_url":"https://api.github.com/users/n1zea144/following{/other_user}","gists_url":"https://api.github.com/users/n1zea144/gists{/gist_id}","starred_url":"https://api.github.com/users/n1zea144/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/n1zea144/subscriptions","organizations_url":"https://api.github.com/users/n1zea144/orgs","repos_url":"https://api.github.com/users/n1zea144/repos","events_url":"https://api.github.com/users/n1zea144/events{/privacy}","received_events_url":"https://api.github.com/users/n1zea144/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2016-03-01T16:00:08Z","updated_at":"2016-03-01T16:00:16Z","closed_at":"2016-03-01T16:00:11Z","body":"*Originally reported by*: @paulclemons\n\nLooks like some of the genes in this page:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#submission/2175456\r\n\r\nrefer to mouse genes in the website, but I'm not sure that was the submitter intent (Ken in one case, Karin in others)\r\n\r\nBenjamin and I talked about a couple of these on the phone, but I'm not sure all were resolved, possibly due to case-sensitive versus insensitive matches?:\r\n\r\n**from the telephone discussion (and subsequent email):\r\n**\r\n3. corrected gene symbols -- these three stand as corrected:\r\n3a:  FLJ32065 -> AMZ2P1 is correct per genenames.org (occurs in columbia_marina_analysis)\r\n3c:  FGFR -> FGFR1 is correct per genenames.org (occurs in cshl_tier4_fgf19_story)\r\n3d:  WNT -> WNT1 is correct per genenames.org (occurs in dfci_tier4_beta-catenin_story)\r\n\r\nthis one also is a correct re-assignment,  but I think it happens in a different submission than you report:\r\n3b:  C/EBP -> CEBPA is correct per genenames.org (actually occurs in columbia_mra_fet_analysis rather than columbia_joint_mr_shrna_diff)\r\n\r\nand as discussed these 2 'dropped' ones you were going to add back (since they correctly occur in columbia_tier4_glioma_story):\r\nC/EBPb -> CEBPB is correct per genenames.org (actually occurs in columbia_mra_fet_analysis rather than columbia_joint_mr_shrna_diff)\r\nC/EBPd -> CEBPD is correct per genenames.org (actually occurs in columbia_mra_fet_analysis rather than columbia_joint_mr_shrna_diff)\r\n\r\n\r\n**here's what i find investigating the same genes in the website:**\r\n\r\nFLJ32065 -> AMZ2P1\r\nobservation:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/observation/2167434\r\nappears to be human:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/subject/1486486\r\n\r\n\r\nFGFR -> FGFR1\r\nobservation:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/observation/2177503\r\nappears to map to mouse:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/subject/1595693\r\nrather than human:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#subject/1387397\r\n\r\n\r\nWNT -> WNT1\r\nobservation:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/observation/2177514\r\nappears to (correctly, I think) map to human here:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/subject/1413389\r\nand not to mouse:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#subject/1623075\r\n\r\n\r\nC/EBP -> CEBPA\r\nobservation:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/observation/2175514\r\nappears to map to human:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/subject/1381519\r\nand not to mouse:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#subject/1590156\r\n\r\nC/EBPb -> CEBPB\r\nboth observations:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/observation/2177492\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/observation/2175647\r\nappear to map to human:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/subject/1381524\r\nand not to mouse:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#subject/1590169\r\n\r\nC/EBPd -> CEBPD\r\nboth observations:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/observation/2177492\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#/observation/2175533\r\n\r\nappear to map to mouse:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#subject/1590180\r\nand not to human:\r\nhttp://cbio.mskcc.org/ctd2-dashboard/#subject/1381533\r\n\r\nmaybe this will resolve automatically with a future update of background data and submission data -- are the gene symbol matches case-sensitive in general?\r\n"},"comment":{"url":"https://api.github.com/repos/CBIIT/nci-ctd2-dashboard/issues/comments/190784192","html_url":"https://github.com/CBIIT/nci-ctd2-dashboard/issues/54#issuecomment-190784192","issue_url":"https://api.github.com/repos/CBIIT/nci-ctd2-dashboard/issues/54","id":190784192,"user":{"login":"hermidalc","id":461066,"avatar_url":"https://avatars.githubusercontent.com/u/461066?v=3","gravatar_id":"","url":"https://api.github.com/users/hermidalc","html_url":"https://github.com/hermidalc","followers_url":"https://api.github.com/users/hermidalc/followers","following_url":"https://api.github.com/users/hermidalc/following{/other_user}","gists_url":"https://api.github.com/users/hermidalc/gists{/gist_id}","starred_url":"https://api.github.com/users/hermidalc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hermidalc/subscriptions","organizations_url":"https://api.github.com/users/hermidalc/orgs","repos_url":"https://api.github.com/users/hermidalc/repos","events_url":"https://api.github.com/users/hermidalc/events{/privacy}","received_events_url":"https://api.github.com/users/hermidalc/received_events","type":"User","site_admin":false},"created_at":"2016-03-01T16:00:16Z","updated_at":"2016-03-01T16:00:16Z","body":"*Original comment by*: @paulclemons\n\nbased on quick non-systematic inspection of some of the other observations, it seems that sometimes both human and mouse are mapped (though i think only one is meant by the submitter). Compare:\nhttp://cbio.mskcc.org/ctd2-dashboard/#subject/1377285\nhttp://cbio.mskcc.org/ctd2-dashboard/#subject/1586365\n"}}