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MCL coexpression mm9:72: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.03092442828344,1.00522150063468,1.065057102305,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.015138597952937,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.054943952156948,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5.1030868246177e-05,0,0.0156057243067075,0.0843504501108034,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.03092442828344,1.00522150063468,1.065057102305,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.015138597952937,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.054943952156948,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5.1030868246177e-05,0,0.0156057243067075,0.0843504501108034,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0005102;receptor binding;0.0078642851207815;20311,116903,11839,19227,20195,57349,11876,16878!GO:0005615;extracellular space;0.0078642851207815;20311,11839,67701,19225,57425,19227,20195,216795,11830,12740,16782,11876,16878,70835!GO:0044421;extracellular region part;0.0100560245154138;20311,11839,67701,19225,57425,19227,20195,216795,11830,12740,16782,11876,16878,70835!GO:0005125;cytokine activity;0.0112832883092901;20311,11839,16878,20195,57349!
|gostat_on_MCL_coexpression=GO:0005102;receptor binding;0.0078642851207815;20311,116903,11839,19227,20195,57349,11876,16878!GO:0005615;extracellular space;0.0078642851207815;20311,11839,67701,19225,57425,19227,20195,216795,11830,12740,16782,11876,16878,70835!GO:0044421;extracellular region part;0.0100560245154138;20311,11839,67701,19225,57425,19227,20195,216795,11830,12740,16782,11876,16878,70835!GO:0005125;cytokine activity;0.0112832883092901;20311,11839,16878,20195,57349!
|ontology_enrichment_celltype=CL:0000068!3.67e-34!3;CL:0002202!3.67e-34!3;CL:0000069!3.67e-34!3;CL:0002632!3.67e-34!3;CL:0002368!3.67e-34!3;CL:0000307!3.67e-34!3;CL:0000377!3.67e-34!3;CL:0002076!2.17e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003126!3.67e-34!3;UBERON:0001005!3.67e-34!3;UBERON:0007196!3.67e-34!3;UBERON:0001558!3.67e-34!3;UBERON:0000162!2.41e-15!3;UBERON:0001353!2.41e-15!3;UBERON:0000163!2.41e-15!3;UBERON:0006866!2.41e-15!3;UBERON:0001046!2.41e-15!3;UBERON:0000164!2.41e-15!3;UBERON:0000931!2.41e-15!3;UBERON:0000996!2.59e-12!1;UBERON:0001255!7.11e-12!1;UBERON:0001556!7.11e-12!1;UBERON:0003975!1.20e-09!5;UBERON:0000161!1.33e-09!5;UBERON:0004122!1.33e-09!5
}}
}}

Revision as of 21:08, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:74636711..74636725,+p2@Bcr
Mm9::chr11:100002128..100002131,+p@chr11:100002128..100002131
+
Mm9::chr11:100002209..100002231,+p@chr11:100002209..100002231
+
Mm9::chr11:100002237..100002272,+p@chr11:100002237..100002272
+
Mm9::chr11:100002314..100002327,+p@chr11:100002314..100002327
+
Mm9::chr11:100002838..100002881,+p@chr11:100002838..100002881
+
Mm9::chr11:100002992..100003004,-p@chr11:100002992..100003004
-
Mm9::chr11:100006864..100006873,+p@chr11:100006864..100006873
+
Mm9::chr11:29642912..29642916,-p@chr11:29642912..29642916
-
Mm9::chr11:4164303..4164316,+p@chr11:4164303..4164316
+
Mm9::chr11:4165247..4165267,+p@chr11:4165247..4165267
+
Mm9::chr11:4166670..4166676,+p4@Lif
Mm9::chr11:51981619..51981639,-p@chr11:51981619..51981639
-
Mm9::chr11:59120422..59120437,+p1@Wnt9a
Mm9::chr11:62656257..62656262,+p@chr11:62656257..62656262
+
Mm9::chr11:70027607..70027634,+p1@Slc16a11
Mm9::chr11:70027638..70027664,+p3@Slc16a11
Mm9::chr11:86461733..86461747,-p@chr11:86461733..86461747
-
Mm9::chr11:94938259..94938265,+p@chr11:94938259..94938265
+
Mm9::chr11:94958540..94958582,+p@chr11:94958540..94958582
+
Mm9::chr11:96608719..96608730,-p1@ENSMUST00000170876
p1@uc011ydj.1
Mm9::chr11:96608733..96608746,-p1@ENSMUST00000166907
Mm9::chr11:96608968..96608974,-p2@ENSMUST00000166907
Mm9::chr11:98561479..98561520,+p@chr11:98561479..98561520
+
Mm9::chr12:17549752..17549763,+p@chr12:17549752..17549763
+
Mm9::chr12:80660732..80660753,+p@chr12:80660732..80660753
+
Mm9::chr12:82732215..82732299,+p1@Ttc9
Mm9::chr12:8799233..8799252,+p@chr12:8799233..8799252
+
Mm9::chr13:115644652..115644657,-p@chr13:115644652..115644657
-
Mm9::chr13:115722144..115722156,-p3@Itga2
Mm9::chr13:115722243..115722274,-p1@Itga2
Mm9::chr13:115722278..115722317,-p2@Itga2
Mm9::chr13:115722413..115722430,+p@chr13:115722413..115722430
+
Mm9::chr13:49394171..49394182,-p7@Fgd3
Mm9::chr13:72401408..72401416,-p@chr13:72401408..72401416
-
Mm9::chr14:21662458..21662463,+p@chr14:21662458..21662463
+
Mm9::chr14:31386795..31386797,-p@chr14:31386795..31386797
-
Mm9::chr14:34905716..34905718,+p@chr14:34905716..34905718
+
Mm9::chr14:43799688..43799691,-p@chr14:43799688..43799691
-
Mm9::chr14:66120363..66120367,+p@chr14:66120363..66120367
+
Mm9::chr14:66592250..66592264,-p@chr14:66592250..66592264
-
Mm9::chr14:66592291..66592317,-p@chr14:66592291..66592317
-
Mm9::chr14:66593827..66593846,-p@chr14:66593827..66593846
-
Mm9::chr14:66599823..66599861,-p@chr14:66599823..66599861
-
Mm9::chr14:66600371..66600386,-p@chr14:66600371..66600386
-
Mm9::chr14:75132109..75132181,+p1@Esd
p1@Gm2904
Mm9::chr15:101242848..101242864,+p1@Krt7
Mm9::chr15:101248779..101248798,-p@chr15:101248779..101248798
-
Mm9::chr15:101248802..101248828,-p@chr15:101248802..101248828
-
Mm9::chr15:101250936..101250949,+p@chr15:101250936..101250949
+
Mm9::chr15:101258041..101258052,+p@chr15:101258041..101258052
+
Mm9::chr15:74789738..74789763,-p@chr15:74789738..74789763
-
Mm9::chr15:74825521..74825542,-p@chr15:74825521..74825542
-
Mm9::chr15:74825821..74825827,+p@chr15:74825821..74825827
+
Mm9::chr15:99421285..99421330,-p@chr15:99421285..99421330
-
Mm9::chr15:99421567..99421581,+p1@Aqp5
Mm9::chr16:10960551..10960554,-p@chr16:10960551..10960554
-
Mm9::chr16:32641594..32641601,+p@chr16:32641594..32641601
+
Mm9::chr16:43664217..43664239,-p1@Tigit
Mm9::chr17:23812818..23812855,-p@chr17:23812818..23812855
-
Mm9::chr17:24135061..24135076,-p1@Prss22
Mm9::chr17:25885558..25885567,+p@chr17:25885558..25885567
+
Mm9::chr17:25890993..25891014,-p@chr17:25890993..25891014
-
Mm9::chr17:35195662..35195665,-p@chr17:35195662..35195665
-
Mm9::chr17:71089456..71089459,-p@chr17:71089456..71089459
-
Mm9::chr17:71105425..71105430,+p@chr17:71105425..71105430
+
Mm9::chr18:16433080..16433097,+p@chr18:16433080..16433097
+
Mm9::chr19:30033557..30033562,+p@chr19:30033557..30033562
+
Mm9::chr19:30034003..30034011,+p@chr19:30034003..30034011
+
Mm9::chr19:38171348..38171379,+p2@O3far1
Mm9::chr19:38171555..38171594,+p1@O3far1
Mm9::chr19:47583250..47583267,-p5@Obfc1
Mm9::chr19:47932377..47932386,-p@chr19:47932377..47932386
-
Mm9::chr19:47932481..47932497,+p@chr19:47932481..47932497
+
Mm9::chr19:47937865..47937876,+p7@Gsto1
Mm9::chr19:47938904..47938922,-p@chr19:47938904..47938922
-
Mm9::chr19:47938927..47938952,-p@chr19:47938927..47938952
-
Mm9::chr19:47939269..47939279,-p@chr19:47939269..47939279
-
Mm9::chr1:108303887..108303893,+p@chr1:108303887..108303893
+
Mm9::chr1:137741978..137741989,+p@chr1:137741978..137741989
+
Mm9::chr1:151947223..151947236,+p1@Ptgs2
Mm9::chr1:151954385..151954387,+p@chr1:151954385..151954387
+
Mm9::chr1:152012073..152012094,-p2@ENSMUST00000163840
Mm9::chr1:152012112..152012121,-p6@ENSMUST00000163840
Mm9::chr1:155033141..155033186,-p@chr1:155033141..155033186
-
Mm9::chr1:40556854..40556870,+p@chr1:40556854..40556870
+
Mm9::chr1:60762131..60762139,+p@chr1:60762131..60762139
+
Mm9::chr1:72429924..72429941,+p@chr1:72429924..72429941
+
Mm9::chr2:102653606..102653626,-p@chr2:102653606..102653626
-
Mm9::chr2:103103766..103103770,-p@chr2:103103766..103103770
-
Mm9::chr2:117952400..117952414,+p@chr2:117952400..117952414
+
Mm9::chr2:117952457..117952476,+p@chr2:117952457..117952476
+
Mm9::chr2:130523198..130523217,-p1@Slc4a11
Mm9::chr2:132771413..132771424,-p6@Fermt1
Mm9::chr2:132771496..132771508,-p7@Fermt1
Mm9::chr2:132771611..132771620,-p12@Fermt1
Mm9::chr2:144564146..144564166,+p3@Dtd1
Mm9::chr2:164388207..164388221,+p1@Wfdc2
Mm9::chr2:164389604..164389615,+p@chr2:164389604..164389615
+
Mm9::chr2:164393992..164394012,-p@chr2:164393992..164394012
-
Mm9::chr2:60538178..60538182,-p@chr2:60538178..60538182
-
Mm9::chr2:73160809..73160811,+p@chr2:73160809..73160811
+
Mm9::chr2:83646739..83646758,+p@chr2:83646739..83646758
+
Mm9::chr3:121426433..121426452,+p2@F3
Mm9::chr3:121426498..121426503,+p4@F3
Mm9::chr3:121426519..121426536,+p1@F3
Mm9::chr3:121437538..121437546,+p@chr3:121437538..121437546
+
Mm9::chr3:121437587..121437593,+p@chr3:121437587..121437593
+
Mm9::chr3:122094760..122094780,-p@chr3:122094760..122094780
-
Mm9::chr3:131670443..131670456,+p@chr3:131670443..131670456
+
Mm9::chr3:89487103..89487111,-p@chr3:89487103..89487111
-
Mm9::chr3:90330696..90330701,+p4@S100a14
Mm9::chr3:90341213..90341226,+p8@S100a16
Mm9::chr3:90392458..90392472,+p@chr3:90392458..90392472
+
Mm9::chr3:90417441..90417458,+p@chr3:90417441..90417458
+
Mm9::chr3:90418268..90418279,+p@chr3:90418268..90418279
+
Mm9::chr3:90418333..90418337,-p@chr3:90418333..90418337
-
Mm9::chr3:95539830..95539861,+p@chr3:95539830..95539861
+
Mm9::chr3:95540003..95540044,-p@chr3:95540003..95540044
-
Mm9::chr3:95540043..95540066,+p@chr3:95540043..95540066
+
Mm9::chr3:95540093..95540105,+p@chr3:95540093..95540105
+
Mm9::chr3:95540608..95540642,-p@chr3:95540608..95540642
-
Mm9::chr4:117602071..117602080,-p2@Artn
Mm9::chr4:154956870..154956881,+p4@Nadk
Mm9::chr4:88563148..88563158,-p@chr4:88563148..88563158
-
Mm9::chr4:88563185..88563192,-p@chr4:88563185..88563192
-
Mm9::chr4:88696144..88696152,+p3@Gm12603
Mm9::chr4:88696177..88696184,+p2@Gm12603
Mm9::chr4:88696200..88696228,+p1@Gm12603
Mm9::chr5:103804464..103804467,+p@chr5:103804464..103804467
+
Mm9::chr5:125866346..125866349,+p@chr5:125866346..125866349
+
Mm9::chr5:135420996..135421000,+p@chr5:135420996..135421000
+
Mm9::chr5:135421121..135421128,-p@chr5:135421121..135421128
-
Mm9::chr5:135421686..135421706,-p@chr5:135421686..135421706
-
Mm9::chr5:135421891..135421901,-p@chr5:135421891..135421901
-
Mm9::chr5:135422125..135422141,-p@chr5:135422125..135422141
-
Mm9::chr5:135422309..135422313,-p@chr5:135422309..135422313
-
Mm9::chr5:35341760..35341766,+p12@Rgs12
Mm9::chr5:58617856..58617867,+p@chr5:58617856..58617867
+
Mm9::chr5:73797457..73797507,+p1@Cwh43
Mm9::chr5:91188375..91188393,+p1@Cxcl5
Mm9::chr5:91197537..91197552,+p1@Ppbp
Mm9::chr5:91198477..91198490,+p@chr5:91198477..91198490
+
Mm9::chr5:91198620..91198632,+p@chr5:91198620..91198632
+
Mm9::chr5:91198876..91198885,+p@chr5:91198876..91198885
+
Mm9::chr5:91199084..91199088,-p@chr5:91199084..91199088
-
Mm9::chr5:91568617..91568633,+p1@Areg
Mm9::chr5:91570078..91570084,+p@chr5:91570078..91570084
+
Mm9::chr5:92644371..92644380,-p1@U90926
Mm9::chr5:97225101..97225112,+p@chr5:97225101..97225112
+
Mm9::chr6:122550396..122550400,-p5@Apobec1
Mm9::chr6:125410606..125410617,-p@chr6:125410606..125410617
-
Mm9::chr6:125410674..125410686,-p@chr6:125410674..125410686
-
Mm9::chr6:135034088..135034101,+p@chr6:135034088..135034101
+
Mm9::chr6:142287510..142287516,-p@chr6:142287510..142287516
-
Mm9::chr6:147205603..147205610,+p@chr6:147205603..147205610
+
Mm9::chr6:147205677..147205683,+p@chr6:147205677..147205683
+
Mm9::chr6:147212380..147212396,-p1@Pthlh
Mm9::chr6:147212455..147212462,-p6@Pthlh
Mm9::chr6:147212485..147212499,-p4@Pthlh
Mm9::chr6:147212504..147212550,-p2@Pthlh
Mm9::chr6:147212620..147212625,+p@chr6:147212620..147212625
+
Mm9::chr6:147212646..147212674,-p3@Pthlh
Mm9::chr6:147338308..147338339,-p@chr6:147338308..147338339
-
Mm9::chr6:29490887..29490891,+p5@Irf5
Mm9::chr6:50331651..50331654,-p@chr6:50331651..50331654
-
Mm9::chr6:50332830..50332846,-p2@Osbpl3
Mm9::chr7:116780936..116780950,-p@chr7:116780936..116780950
-
Mm9::chr7:119570539..119570552,+p7@Parva
Mm9::chr7:121862157..121862175,+p1@Calcb
Mm9::chr7:121866295..121866309,+p@chr7:121866295..121866309
+
Mm9::chr7:133766759..133766769,+p@chr7:133766759..133766769
+
Mm9::chr7:19929891..19929904,+p6@Ercc1
Mm9::chr7:77505410..77505426,+p@chr7:77505410..77505426
+
Mm9::chr8:109079897..109079901,+p@chr8:109079897..109079901
+
Mm9::chr8:32217083..32217090,+p@chr8:32217083..32217090
+
Mm9::chr8:74047419..74047426,+p1@ENSMUST00000166830
Mm9::chr8:74226505..74226533,-p@chr8:74226505..74226533
-
Mm9::chr9:108239609..108239630,+p@chr9:108239609..108239630
+
Mm9::chr9:110941233..110941240,+p@chr9:110941233..110941240
+
Mm9::chr9:110941246..110941254,+p@chr9:110941246..110941254
+
Mm9::chrX:153315992..153315996,+p@chrX:153315992..153315996
+
Mm9::chrX:163645025..163645028,+p@chrX:163645025..163645028
+
Mm9::chrX:163647400..163647406,-p5@Tmsb4x
Mm9::chrX:20383628..20383635,+p@chrX:20383628..20383635
+
Mm9::chrX:73088313..73088332,-p4@Pls3


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0005102receptor binding0.0078642851207815
GO:0005615extracellular space0.0078642851207815
GO:0044421extracellular region part0.0100560245154138
GO:0005125cytokine activity0.0112832883092901



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
trachea3.67e-343
respiratory airway3.67e-343
tracheobronchial tree3.67e-343
lower respiratory tract3.67e-343
cloaca2.41e-153
anal region2.41e-153
embryonic cloaca2.41e-153
terminal part of digestive tract2.41e-153
hindgut2.41e-153
primitive urogenital sinus2.41e-153
proctodeum2.41e-153
vagina2.59e-121
urinary bladder7.11e-121
lower urinary tract7.11e-121
internal female genitalia1.20e-095
orifice1.33e-095
genitourinary system1.33e-095


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)

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