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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!9.92e-13!54;UBERON:0001049!2.39e-11!52;UBERON:0005068!2.39e-11!52;UBERON:0006241!2.39e-11!52;UBERON:0007135!2.39e-11!52;UBERON:0002370!1.04e-10!23;UBERON:0000974!1.04e-10!23;UBERON:0004807!1.04e-10!23;UBERON:0005058!1.04e-10!23;UBERON:0003351!1.04e-10!23;UBERON:0009113!1.04e-10!23;UBERON:0003295!1.04e-10!23;UBERON:0009722!1.04e-10!23;UBERON:0005562!1.04e-10!23;UBERON:0007690!1.04e-10!23;UBERON:0006562!6.58e-10!24;UBERON:0003408!6.58e-10!24;UBERON:0001557!6.58e-10!24;UBERON:0001042!6.58e-10!24;UBERON:0008814!6.58e-10!24;UBERON:0009145!6.58e-10!24;UBERON:0000955!1.04e-09!47;UBERON:0006238!1.04e-09!47;UBERON:0001017!1.48e-09!73;UBERON:0010371!2.42e-09!73;UBERON:0002616!2.92e-09!46;UBERON:0002346!6.12e-09!64;UBERON:0003075!6.12e-09!64;UBERON:0007284!6.12e-09!64;UBERON:0001016!7.06e-09!75;UBERON:0002021!7.64e-09!10;UBERON:0000411!7.64e-09!10;UBERON:0001950!7.64e-09!10;UBERON:0000063!8.33e-09!35;UBERON:0002020!1.07e-08!34;UBERON:0000064!1.53e-08!99;UBERON:0004121!3.17e-08!95;UBERON:0000924!3.17e-08!95;UBERON:0006601!3.17e-08!95;UBERON:0000072!6.61e-08!27;UBERON:0002619!1.19e-07!17;UBERON:0003080!2.50e-07!40;UBERON:0003528!3.30e-07!29;UBERON:0002791!3.30e-07!29;UBERON:0001893!3.30e-07!29;UBERON:0004177!7.78e-07!29;UBERON:0005057!7.78e-07!29;UBERON:0002780!8.02e-07!39;UBERON:0001890!8.02e-07!39;UBERON:0006240!8.02e-07!39
|ontology_enrichment_uberon=UBERON:0000073!9.92e-13!54;UBERON:0001049!2.39e-11!52;UBERON:0005068!2.39e-11!52;UBERON:0006241!2.39e-11!52;UBERON:0007135!2.39e-11!52;UBERON:0002370!1.04e-10!23;UBERON:0000974!1.04e-10!23;UBERON:0004807!1.04e-10!23;UBERON:0005058!1.04e-10!23;UBERON:0003351!1.04e-10!23;UBERON:0009113!1.04e-10!23;UBERON:0003295!1.04e-10!23;UBERON:0009722!1.04e-10!23;UBERON:0005562!1.04e-10!23;UBERON:0007690!1.04e-10!23;UBERON:0006562!6.58e-10!24;UBERON:0003408!6.58e-10!24;UBERON:0001557!6.58e-10!24;UBERON:0001042!6.58e-10!24;UBERON:0008814!6.58e-10!24;UBERON:0009145!6.58e-10!24;UBERON:0000955!1.04e-09!47;UBERON:0006238!1.04e-09!47;UBERON:0001017!1.48e-09!73;UBERON:0010371!2.42e-09!73;UBERON:0002616!2.92e-09!46;UBERON:0002346!6.12e-09!64;UBERON:0003075!6.12e-09!64;UBERON:0007284!6.12e-09!64;UBERON:0001016!7.06e-09!75;UBERON:0002021!7.64e-09!10;UBERON:0000411!7.64e-09!10;UBERON:0001950!7.64e-09!10;UBERON:0000063!8.33e-09!35;UBERON:0002020!1.07e-08!34;UBERON:0000064!1.53e-08!99;UBERON:0004121!3.17e-08!95;UBERON:0000924!3.17e-08!95;UBERON:0006601!3.17e-08!95;UBERON:0000072!6.61e-08!27;UBERON:0002619!1.19e-07!17;UBERON:0003080!2.50e-07!40;UBERON:0003528!3.30e-07!29;UBERON:0002791!3.30e-07!29;UBERON:0001893!3.30e-07!29;UBERON:0004177!7.78e-07!29;UBERON:0005057!7.78e-07!29;UBERON:0002780!8.02e-07!39;UBERON:0001890!8.02e-07!39;UBERON:0006240!8.02e-07!39
|tfbs_overrepresentation_for_novel_motifs=0.354643,1.42997,0.330161,0.394491,0.645379,1.05171,0.495658,0.448965,1.46248,0.133458,2.00501,0.484001,0.449446,0.507558,0.24249,0,0.696644,0.22065,0.134657,0.902262,0.296085,1.09871,0.50668,0.226287,0.337218,0.534339,0.402559,0.428336,0.268347,1.61135,0.414842,0.796599,0.624261,0.364174,0.242923,0.281474,0.210533,0.480503,0.191662,0.167387,0.637027,0.419787,0.0422275,1.2686,0.059071,0.383899,0.618203,0.443479,0.133514,0.271021,1.62723,0.560572,1.05886,0.937018,0.954342,0.514504,0.279148,0.471658,1.83156,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.0512949,0.987652,0.116281,0.710896,3.08168,0.607043,0.759798,0.299972,0.463363,0.713779,0.568383,0.14134,0.873141,0.0800961,0.0211263,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.515495,0.871972,0.812053,0.618454,2.02396,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.919252,0.921485,0.301014,0.458194,1.16629,0.222515,0.0259088,0.398075,0.697928,0.597328,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,1.23559,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.951467,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.369078,0.938577,0.178329,1.3067,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.602679,0.482466,0.12239
}}
}}

Revision as of 19:00, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr5:107788562..107788605,+p2@Brdt
Mm9::chr9:43851294..43851336,+p2@Thy1
Mm9::chr9:43851473..43851517,+p1@Thy1
Mm9::chr9:43854810..43854849,-p@chr9:43854810..43854849
-
Mm9::chr9:43854871..43854901,+p@chr9:43854871..43854901
+
Mm9::chr9:43854935..43854978,-p@chr9:43854935..43854978
-
Mm9::chr9:43854987..43854999,+p@chr9:43854987..43854999
+
Mm9::chr9:43855655..43855666,+p@chr9:43855655..43855666
+
Mm9::chr9:43856002..43856018,+p@chr9:43856002..43856018
+


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:0042670retinal cone cell differentiation0.00597162110338027
GO:0046549retinal cone cell development0.00597162110338027
GO:0060042retina morphogenesis in camera-type eye0.00716555271254392
GO:0031362anchored to external side of plasma membrane0.00716555271254392
GO:0031233intrinsic to external side of plasma membrane0.00716555271254392
GO:0050858negative regulation of antigen receptor-mediated signaling pathway0.00852995250122804
GO:0050860negative regulation of T cell receptor signaling pathway0.00852995250122804
GO:0042393histone binding0.010103051914287
GO:0060041retina development in camera-type eye0.010103051914287
GO:0050856regulation of T cell receptor signaling pathway0.010103051914287
GO:0031225anchored to membrane0.010103051914287
GO:0046658anchored to plasma membrane0.010103051914287
GO:0050854regulation of antigen receptor-mediated signaling pathway0.010103051914287
GO:0042462eye photoreceptor cell development0.0119376802103351
GO:0001754eye photoreceptor cell differentiation0.0119376802103351
GO:0042461photoreceptor cell development0.0119376802103351
GO:0048593camera-type eye morphogenesis0.0119376802103351
GO:0050852T cell receptor signaling pathway0.0119376802103351
GO:0046530photoreceptor cell differentiation0.0131931932796124
GO:0050851antigen receptor-mediated signaling pathway0.0161118930923894
GO:0002429immune response-activating cell surface receptor signaling pathway0.0181353277613955
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0181353277613955
GO:0002757immune response-activating signal transduction0.0181353277613955
GO:0006338chromatin remodeling0.0181353277613955
GO:0002764immune response-regulating signal transduction0.0181353277613955
GO:0048592eye morphogenesis0.0197295590217139
GO:0043010camera-type eye development0.0327755362301843
GO:0002253activation of immune response0.0327755362301843
GO:0050778positive regulation of immune response0.0389109199577307
GO:0002684positive regulation of immune system process0.0389109199577307
GO:0001654eye development0.0399545960452431
GO:0050776regulation of immune response0.0401367309985071
GO:0002682regulation of immune system process0.0401367309985071
GO:0051240positive regulation of multicellular organismal process0.0401367309985071
GO:0048503GPI anchor binding0.0401367309985071
GO:0001525angiogenesis0.0437371347021604
GO:0009897external side of plasma membrane0.0437371347021604
GO:0016043cellular component organization and biogenesis0.0460427918832516
GO:0035091phosphoinositide binding0.04904453936278
GO:0016568chromatin modification0.04904453936278
GO:0048514blood vessel morphogenesis0.0491152203408847
GO:0009986cell surface0.0491152203408847
GO:0000904cellular morphogenesis during differentiation0.0491152203408847
GO:0048646anatomical structure formation0.0491152203408847
GO:0007423sensory organ development0.0491152203408847



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system9.92e-1354
neural tube2.39e-1152
neural rod2.39e-1152
future spinal cord2.39e-1152
neural keel2.39e-1152
thymus1.04e-1023
neck1.04e-1023
respiratory system epithelium1.04e-1023
hemolymphoid system gland1.04e-1023
pharyngeal epithelium1.04e-1023
thymic region1.04e-1023
pharyngeal gland1.04e-1023
entire pharyngeal arch endoderm1.04e-1023
thymus primordium1.04e-1023
early pharyngeal endoderm1.04e-1023
pharynx6.58e-1024
gland of gut6.58e-1024
upper respiratory tract6.58e-1024
chordate pharynx6.58e-1024
pharyngeal arch system6.58e-1024
pharyngeal region of foregut6.58e-1024
brain1.04e-0947
future brain1.04e-0947
central nervous system1.48e-0973
ecto-epithelium2.42e-0973
regional part of brain2.92e-0946
neurectoderm6.12e-0964
neural plate6.12e-0964
presumptive neural plate6.12e-0964
nervous system7.06e-0975
occipital lobe7.64e-0910
visual cortex7.64e-0910
neocortex7.64e-0910
organ segment8.33e-0935
gray matter1.07e-0834
organ part1.53e-0899
ectoderm-derived structure3.17e-0895
ectoderm3.17e-0895
presumptive ectoderm3.17e-0895
segment of respiratory tract6.61e-0827
regional part of cerebral cortex1.19e-0717
anterior neural tube2.50e-0740
brain grey matter3.30e-0729
regional part of telencephalon3.30e-0729
telencephalon3.30e-0729
hemopoietic organ7.78e-0729
immune organ7.78e-0729
regional part of forebrain8.02e-0739
forebrain8.02e-0739
future forebrain8.02e-0739


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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