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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!2.06e-35!29;UBERON:0005057!2.06e-35!29;UBERON:0002370!2.23e-33!23;UBERON:0000974!2.23e-33!23;UBERON:0004807!2.23e-33!23;UBERON:0005058!2.23e-33!23;UBERON:0003351!2.23e-33!23;UBERON:0009113!2.23e-33!23;UBERON:0003295!2.23e-33!23;UBERON:0009722!2.23e-33!23;UBERON:0005562!2.23e-33!23;UBERON:0007690!2.23e-33!23;UBERON:0006562!8.27e-32!24;UBERON:0003408!8.27e-32!24;UBERON:0001557!8.27e-32!24;UBERON:0001042!8.27e-32!24;UBERON:0008814!8.27e-32!24;UBERON:0009145!8.27e-32!24;UBERON:0002193!6.98e-29!48;UBERON:0002405!6.98e-29!48;UBERON:0000077!1.70e-28!35;UBERON:0002390!2.23e-28!45;UBERON:0003061!2.23e-28!45;UBERON:0000072!8.46e-28!27;UBERON:0000065!3.01e-23!41;UBERON:0001004!1.41e-22!42;UBERON:0000063!1.81e-20!35;UBERON:0007811!8.81e-20!36;UBERON:0000153!7.17e-16!43;UBERON:0001041!1.36e-14!80;UBERON:0003081!5.04e-12!87;UBERON:0005911!7.65e-12!69;UBERON:0003929!1.70e-11!55;UBERON:0002368!3.41e-10!60;UBERON:0004921!1.72e-09!114;UBERON:0001007!3.15e-09!116;UBERON:0001555!3.15e-09!116;UBERON:0007026!3.15e-09!116;UBERON:0002530!4.28e-09!65;UBERON:0004119!5.64e-09!118;UBERON:0000925!5.64e-09!118;UBERON:0006595!5.64e-09!118;UBERON:0000490!6.76e-09!66;UBERON:0000064!7.95e-09!99;UBERON:0000949!8.06e-08!72;UBERON:0002384!2.61e-07!46;UBERON:0000926!3.08e-07!120;UBERON:0004120!3.08e-07!120;UBERON:0006603!3.08e-07!120
|ontology_enrichment_uberon=UBERON:0004177!2.06e-35!29;UBERON:0005057!2.06e-35!29;UBERON:0002370!2.23e-33!23;UBERON:0000974!2.23e-33!23;UBERON:0004807!2.23e-33!23;UBERON:0005058!2.23e-33!23;UBERON:0003351!2.23e-33!23;UBERON:0009113!2.23e-33!23;UBERON:0003295!2.23e-33!23;UBERON:0009722!2.23e-33!23;UBERON:0005562!2.23e-33!23;UBERON:0007690!2.23e-33!23;UBERON:0006562!8.27e-32!24;UBERON:0003408!8.27e-32!24;UBERON:0001557!8.27e-32!24;UBERON:0001042!8.27e-32!24;UBERON:0008814!8.27e-32!24;UBERON:0009145!8.27e-32!24;UBERON:0002193!6.98e-29!48;UBERON:0002405!6.98e-29!48;UBERON:0000077!1.70e-28!35;UBERON:0002390!2.23e-28!45;UBERON:0003061!2.23e-28!45;UBERON:0000072!8.46e-28!27;UBERON:0000065!3.01e-23!41;UBERON:0001004!1.41e-22!42;UBERON:0000063!1.81e-20!35;UBERON:0007811!8.81e-20!36;UBERON:0000153!7.17e-16!43;UBERON:0001041!1.36e-14!80;UBERON:0003081!5.04e-12!87;UBERON:0005911!7.65e-12!69;UBERON:0003929!1.70e-11!55;UBERON:0002368!3.41e-10!60;UBERON:0004921!1.72e-09!114;UBERON:0001007!3.15e-09!116;UBERON:0001555!3.15e-09!116;UBERON:0007026!3.15e-09!116;UBERON:0002530!4.28e-09!65;UBERON:0004119!5.64e-09!118;UBERON:0000925!5.64e-09!118;UBERON:0006595!5.64e-09!118;UBERON:0000490!6.76e-09!66;UBERON:0000064!7.95e-09!99;UBERON:0000949!8.06e-08!72;UBERON:0002384!2.61e-07!46;UBERON:0000926!3.08e-07!120;UBERON:0004120!3.08e-07!120;UBERON:0006603!3.08e-07!120
|tfbs_overrepresentation_for_novel_motifs=0.0772209,0.211545,0.234103,1.09899,0.821971,0.341268,0.156184,1.00142,0.489306,0.370373,0.407767,0.890574,0.704159,0.163767,0.308138,0,0.298759,0.108166,0.10903,0.421075,0.746821,0.0803384,0.163204,0.0271459,0.243279,0.181283,0.0993251,0.370572,0.65112,0.0569143,0.712345,0.987057,0.48539,0.173722,0.0322491,0.682953,0.0227233,0.146713,0.399193,0.162622,0.805467,0.11102,0.215975,0.899572,0.0151228,0.306585,0.239777,0.393105,0.522879,0.369578,0.285502,0.199013,0.384084,0.498054,0.513233,0.503032,0.688152,0.435923,0.808182,0.166967,0.362491,0.205372,0.531917,0.277045,0.175326,0.307787,0.634702,0.961967,0.358731,0.821947,0.0582314,0.0490158,0.000470764,0.542659,0.0823992,0.979638,0.747297,0.2317,0.348727,1.6338,0.0497067,0.312115,0.204396,0.433894,0.442898,1.9281e-05,0.0180686,0.618732,0.243285,1.11866,0.698467,0.447112,0.389188,0.846363,0.0781271,1.59959,0.124357,0.391493,0.674146,0.328957,0.743159,0.378494,0.482983,0.285951,0.778117,0.110785,0.331187,0.775412,0.20165,0.193419,1.3942,0.484521,1.16824,0.133166,1.68031,0.497898,0.0102731,0.670201,0.299754,0.095335,0.547427,0.261521,0.182466,0.23106,0.755173,0.35168,0.161211,0.38364,0.633325,0.293629,0.468394,1.07367,0.606596,0.524274,0.72494,0.744667,0.982953,0.728285,0.679593,1.47999,1.08773,0.638981,1.6721,1.00582,0.280284,0.725963,0.242008,1.44084,0.082151,0.280553,0.0590717,0.000256848,0.499416,0.596474,1.59254,0.571287,0.579167,0.142068,0.263291,0.0809296,0.688329,0.442174,0.352036,1.38395,0.277809,0.511277,0.0974552,0.147927,0.0074331
}}
}}

Revision as of 18:07, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126603372..126603396,-p@chr10:126603372..126603396
-
Mm9::chr10:126603399..126603414,-p@chr10:126603399..126603414
-
Mm9::chr14:54150421..54150439,+p1@uc007tsm.1
Mm9::chr14:54788225..54788236,+p2@uc007tuh.1
Mm9::chr14:54794275..54794301,+p@chr14:54794275..54794301
+
Mm9::chr14:54805521..54805526,+p@chr14:54805521..54805526
+
Mm9::chr14:54811931..54811962,+p1@uc007tuv.2
Mm9::chr14:54813895..54813913,+p@chr14:54813895..54813913
+
Mm9::chr16:23175296..23175310,+p3@uc007ytl.1
Mm9::chr17:35068849..35068882,+p3@Neu1
Mm9::chr18:89366813..89366837,+p1@Cd226
Mm9::chr18:89366845..89366851,+p8@Cd226
Mm9::chr1:138476217..138476228,+p@chr1:138476217..138476228
+
Mm9::chr2:156665551..156665562,+p6@Tgif2
Mm9::chr3:106286353..106286355,-p1@ENSMUST00000164330
Mm9::chr3:106288821..106288844,-p2@2010016I18Rik
Mm9::chr3:106288927..106288975,+p1@Dennd2d
Mm9::chr3:106288977..106289010,+p2@Dennd2d
Mm9::chr4:133674004..133674025,+p@chr4:133674004..133674025
+
Mm9::chr4:133674029..133674037,+p@chr4:133674029..133674037
+
Mm9::chr4:63521926..63521955,-p@chr4:63521926..63521955
-
Mm9::chr4:63522312..63522327,-p3@Tnfsf8
Mm9::chr4:63522330..63522352,-p4@Tnfsf8
Mm9::chr4:63522360..63522389,-p1@Tnfsf8
Mm9::chr6:48627672..48627688,+p@chr6:48627672..48627688
+
Mm9::chr7:134288117..134288146,-p@chr7:134288117..134288146
-
Mm9::chr9:32525693..32525698,-p@chr9:32525693..32525698
-
Mm9::chr9:40812645..40812656,-p@chr9:40812645..40812656
-


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:0002423natural killer cell mediated immune response to tumor cell0.00481183074451149
GO:0002855regulation of natural killer cell mediated immune response to tumor cell0.00481183074451149
GO:0002420natural killer cell mediated cytotoxicity directed against tumor cell target0.00481183074451149
GO:0002858regulation of natural killer cell mediated cytotoxicity directed against tumor cell target0.00481183074451149
GO:0002860positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target0.00481183074451149
GO:0002715regulation of natural killer cell mediated immunity0.00481183074451149
GO:0002857positive regulation of natural killer cell mediated immune response to tumor cell0.00481183074451149
GO:0002717positive regulation of natural killer cell mediated immunity0.00481183074451149
GO:0002355detection of tumor cell0.00481183074451149
GO:0001816cytokine production0.00481183074451149
GO:0050715positive regulation of cytokine secretion0.0083165258331406
GO:0050714positive regulation of protein secretion0.00952622026592251
GO:0007288sperm axoneme assembly0.00952622026592251
GO:0035084flagellum axoneme biogenesis0.00952622026592251
GO:0002831regulation of response to biotic stimulus0.00952622026592251
GO:0002833positive regulation of response to biotic stimulus0.00952622026592251
GO:0050707regulation of cytokine secretion0.00952622026592251
GO:0002836positive regulation of response to tumor cell0.00952622026592251
GO:0002837regulation of immune response to tumor cell0.00952622026592251
GO:0002839positive regulation of immune response to tumor cell0.00952622026592251
GO:0009595detection of biotic stimulus0.00952622026592251
GO:0035082axoneme biogenesis0.00952622026592251
GO:0002834regulation of response to tumor cell0.00952622026592251
GO:0002418immune response to tumor cell0.00952622026592251
GO:0009296flagellum biogenesis0.0105509646398961
GO:0050663cytokine secretion0.0105509646398961
GO:0002347response to tumor cell0.0114289592046159
GO:0043064flagellum organization and biogenesis0.0114289592046159
GO:0048584positive regulation of response to stimulus0.0126098834243107
GO:0001578microtubule bundle formation0.0132694311939168
GO:0045954positive regulation of natural killer cell mediated cytotoxicity0.0132694311939168
GO:0051047positive regulation of secretion0.0142815032029731
GO:0042269regulation of natural killer cell mediated cytotoxicity0.0161261630405946
GO:0001912positive regulation of leukocyte mediated cytotoxicity0.0161261630405946
GO:0050708regulation of protein secretion0.0163127774808018
GO:0042267natural killer cell mediated cytotoxicity0.0163127774808018
GO:0002705positive regulation of leukocyte mediated immunity0.0163127774808018
GO:0001910regulation of leukocyte mediated cytotoxicity0.0163127774808018
GO:0007595lactation0.0163127774808018
GO:0031341regulation of cell killing0.0163127774808018
GO:0002708positive regulation of lymphocyte mediated immunity0.0163127774808018
GO:0002228natural killer cell mediated immunity0.0163127774808018
GO:0002699positive regulation of immune effector process0.0169937756025796
GO:0002703regulation of leukocyte mediated immunity0.0172515121539335
GO:0002706regulation of lymphocyte mediated immunity0.0172515121539335
GO:0005164tumor necrosis factor receptor binding0.0174871009337694
GO:0032813tumor necrosis factor receptor superfamily binding0.0174871009337694
GO:0002697regulation of immune effector process0.0180720717382586
GO:0030317sperm motility0.0195624664669679
GO:0001906cell killing0.0196881681189481
GO:0001909leukocyte mediated cytotoxicity0.0196881681189481
GO:0006955immune response0.0207701369682652
GO:0009306protein secretion0.0258117505595694
GO:0005102receptor binding0.0302297207628627
GO:0007286spermatid development0.0345406479594895
GO:0008037cell recognition0.0345406479594895
GO:0048515spermatid differentiation0.0345406479594895
GO:0048583regulation of response to stimulus0.0345406479594895
GO:0030031cell projection biogenesis0.0370258177043377
GO:0051046regulation of secretion0.039081647890833
GO:0002376immune system process0.039081647890833
GO:0000226microtubule cytoskeleton organization and biogenesis0.0468966974512348
GO:0005515protein binding0.0481297991126234
GO:0051606detection of stimulus0.0488354565099019
GO:0048609reproductive process in a multicellular organism0.0488354565099019
GO:0032504multicellular organism reproduction0.0488354565099019



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>

Cell Type
Ontology termp-valuen
mature alpha-beta T cell9.96e-259
alpha-beta T cell9.96e-259
immature T cell9.96e-259
mature T cell9.96e-259
immature alpha-beta T cell9.96e-259
CD4-positive, alpha-beta T cell3.64e-228
lymphoid lineage restricted progenitor cell9.40e-2212
lymphocyte6.49e-2013
common lymphoid progenitor6.49e-2013
T cell6.80e-2011
pro-T cell6.80e-2011
thymocyte4.84e-176
double negative thymocyte4.84e-176
naive T cell4.84e-176
double-positive, alpha-beta thymocyte4.84e-176
CD4-positive, alpha-beta thymocyte4.84e-176
naive thymus-derived CD4-positive, alpha-beta T cell4.84e-176
DN4 thymocyte4.84e-176
DN1 thymic pro-T cell4.84e-176
DN2 thymocyte4.84e-176
DN3 thymocyte4.84e-176
immature single positive thymocyte4.84e-176
early T lineage precursor4.84e-176
mature CD4 single-positive thymocyte4.84e-176
resting double-positive thymocyte4.84e-176
double-positive blast4.84e-176
CD69-positive double-positive thymocyte4.84e-176
CD69-positive, CD4-positive single-positive thymocyte4.84e-176
CD4-positive, CD8-intermediate double-positive thymocyte4.84e-176
CD24-positive, CD4 single-positive thymocyte4.84e-176
hematopoietic lineage restricted progenitor cell6.74e-1625
nucleate cell8.89e-1616
leukocyte1.01e-1417
nongranular leukocyte1.01e-1417
hematopoietic cell9.09e-1232
hematopoietic oligopotent progenitor cell9.09e-1232
hematopoietic stem cell9.09e-1232
angioblastic mesenchymal cell9.09e-1232
hematopoietic multipotent progenitor cell9.09e-1232
connective tissue cell2.61e-0746
mesenchymal cell2.61e-0746

Uber Anatomy
Ontology termp-valuen
hemopoietic organ2.06e-3529
immune organ2.06e-3529
thymus2.23e-3323
neck2.23e-3323
respiratory system epithelium2.23e-3323
hemolymphoid system gland2.23e-3323
pharyngeal epithelium2.23e-3323
thymic region2.23e-3323
pharyngeal gland2.23e-3323
entire pharyngeal arch endoderm2.23e-3323
thymus primordium2.23e-3323
early pharyngeal endoderm2.23e-3323
pharynx8.27e-3224
gland of gut8.27e-3224
upper respiratory tract8.27e-3224
chordate pharynx8.27e-3224
pharyngeal arch system8.27e-3224
pharyngeal region of foregut8.27e-3224
hemolymphoid system6.98e-2948
immune system6.98e-2948
mixed endoderm/mesoderm-derived structure1.70e-2835
hematopoietic system2.23e-2845
blood island2.23e-2845
segment of respiratory tract8.46e-2827
respiratory tract3.01e-2341
respiratory system1.41e-2242
organ segment1.81e-2035
craniocervical region8.81e-2036
anterior region of body7.17e-1643
foregut1.36e-1480
lateral plate mesoderm5.04e-1287
endo-epithelium7.65e-1269
gut epithelium1.70e-1155
endocrine gland3.41e-1060
subdivision of digestive tract1.72e-09114
digestive system3.15e-09116
digestive tract3.15e-09116
primitive gut3.15e-09116
gland4.28e-0965
endoderm-derived structure5.64e-09118
endoderm5.64e-09118
presumptive endoderm5.64e-09118
unilaminar epithelium6.76e-0966
organ part7.95e-0999
endocrine system8.06e-0872
connective tissue2.61e-0746
mesoderm3.08e-07120
mesoderm-derived structure3.08e-07120
presumptive mesoderm3.08e-07120


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)

{{{tfbs_overrepresentation_jaspar}}}

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