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Coexpression cluster:C2670: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0004923!leukemia inhibitory factor receptor activity!0.0046508889673849!3977$GO:0030552!cAMP binding!0.022470032592992!11069$GO:0016208!AMP binding!0.022470032592992!11069$GO:0005952!cAMP-dependent protein kinase complex!0.022470032592992!11069$GO:0030551!cyclic nucleotide binding!0.022470032592992!11069$GO:0008603!cAMP-dependent protein kinase regulator activity!0.022470032592992!11069$GO:0004896!hematopoietin/interferon-class (D200-domain) cytokine receptor activity!0.0457985933512357!3977
|gostat_on_coexpression_clusters=GO:0004923!leukemia inhibitory factor receptor activity!0.0046508889673849!3977$GO:0030552!cAMP binding!0.022470032592992!11069$GO:0016208!AMP binding!0.022470032592992!11069$GO:0005952!cAMP-dependent protein kinase complex!0.022470032592992!11069$GO:0030551!cyclic nucleotide binding!0.022470032592992!11069$GO:0008603!cAMP-dependent protein kinase regulator activity!0.022470032592992!11069$GO:0004896!hematopoietin/interferon-class (D200-domain) cytokine receptor activity!0.0457985933512357!3977
|id=C2670
|id=C2670
|ontology_enrichment_celltype=CL:0002139!7.56e-15!24;CL:0000115!2.22e-11!35;CL:0000071!4.98e-11!18;CL:0002546!4.98e-11!18;CL:0002078!3.01e-09!44
|ontology_enrichment_celltype=CL:0002139!5.68e-10!24
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!6.05e-62!115;UBERON:0004111!1.59e-28!241;UBERON:0000477!2.07e-28!286;UBERON:0001049!1.29e-26!57;UBERON:0005068!1.29e-26!57;UBERON:0006241!1.29e-26!57;UBERON:0007135!1.29e-26!57;UBERON:0000025!2.41e-25!194;UBERON:0002616!4.72e-23!59;UBERON:0003080!7.49e-22!42;UBERON:0002780!5.66e-21!41;UBERON:0001890!5.66e-21!41;UBERON:0006240!5.66e-21!41;UBERON:0001017!1.17e-20!82;UBERON:0005743!7.21e-20!86;UBERON:0000073!4.25e-19!94;UBERON:0001016!4.25e-19!94;UBERON:0003075!1.67e-18!86;UBERON:0007284!1.67e-18!86;UBERON:0000955!1.88e-18!69;UBERON:0006238!1.88e-18!69;UBERON:0002020!9.48e-18!34;UBERON:0003528!9.48e-18!34;UBERON:0002346!1.36e-17!90;UBERON:0001893!1.55e-17!34;UBERON:0002791!6.60e-17!33;UBERON:0001869!1.89e-16!32;UBERON:0002619!6.37e-14!22;UBERON:0000119!1.24e-13!312;UBERON:0000483!2.08e-13!309;UBERON:0001950!9.83e-13!20;UBERON:0000956!1.97e-12!25;UBERON:0000203!1.97e-12!25;UBERON:0003056!2.93e-12!61;UBERON:0001986!4.98e-11!18;UBERON:0004638!4.98e-11!18;UBERON:0004852!4.98e-11!18;UBERON:0000468!3.27e-10!659;UBERON:0000480!3.46e-10!626;UBERON:0000153!5.74e-10!129;UBERON:0007811!5.74e-10!129;UBERON:0000467!6.94e-10!625;UBERON:0000481!1.95e-09!347;UBERON:0000033!6.98e-09!123;UBERON:0004121!1.11e-08!169;UBERON:0000924!1.97e-08!173;UBERON:0006601!1.97e-08!173;UBERON:0000922!4.30e-08!612;UBERON:0000487!6.42e-08!22;UBERON:0000055!9.13e-08!69;UBERON:0002050!2.19e-07!605;UBERON:0005423!2.19e-07!605;UBERON:0004872!2.22e-07!84;UBERON:0002298!3.66e-07!8;UBERON:0006914!4.44e-07!25;UBERON:0000923!4.74e-07!604;UBERON:0005291!4.74e-07!604;UBERON:0006598!4.74e-07!604;UBERON:0002532!4.74e-07!604;UBERON:0002308!6.76e-07!9;UBERON:0000125!6.76e-07!9;UBERON:0001009!8.95e-07!113
|ontology_enrichment_uberon=UBERON:0007023!8.90e-78!114;UBERON:0001049!1.12e-22!56;UBERON:0005068!1.12e-22!56;UBERON:0006241!1.12e-22!56;UBERON:0007135!1.12e-22!56;UBERON:0000477!2.82e-21!373;UBERON:0000073!1.71e-20!53;UBERON:0002616!1.71e-20!53;UBERON:0004111!3.71e-20!240;UBERON:0002780!3.49e-19!41;UBERON:0001890!3.49e-19!41;UBERON:0003080!3.49e-19!41;UBERON:0006240!3.49e-19!41;UBERON:0001893!6.76e-18!34;UBERON:0003528!8.84e-18!34;UBERON:0002020!8.84e-18!34;UBERON:0001017!1.16e-17!81;UBERON:0003075!2.89e-17!82;UBERON:0007284!2.89e-17!82;UBERON:0002346!9.15e-17!86;UBERON:0001016!1.60e-16!89;UBERON:0001869!3.20e-16!32;UBERON:0010314!3.41e-16!132;UBERON:0002791!3.99e-16!32;UBERON:0000025!7.16e-16!192;UBERON:0000955!2.71e-15!68;UBERON:0006238!2.71e-15!68;UBERON:0011216!1.49e-14!223;UBERON:0003056!2.89e-12!61;UBERON:0010371!6.87e-12!104;UBERON:0002619!3.19e-11!22;UBERON:0001950!4.03e-11!20;UBERON:0000956!1.47e-10!25;UBERON:0000203!1.47e-10!25;UBERON:0000481!5.44e-10!342;UBERON:0000468!1.49e-09!656;UBERON:0000125!1.60e-09!9;UBERON:0002308!1.60e-09!9;UBERON:0004121!7.06e-09!171;UBERON:0000924!7.06e-09!171;UBERON:0006601!7.06e-09!171;UBERON:0000483!3.06e-08!306;UBERON:0000467!3.52e-08!624;UBERON:0000480!4.11e-08!625;UBERON:0000119!5.64e-08!309;UBERON:0009663!9.20e-08!7;UBERON:0002420!1.33e-07!9;UBERON:0007245!1.33e-07!9;UBERON:0010009!1.33e-07!9;UBERON:0010011!1.33e-07!9;UBERON:0000454!1.33e-07!9;UBERON:0003103!1.98e-07!68;UBERON:0000922!3.54e-07!592;UBERON:0002050!6.60e-07!564;UBERON:0000062!8.56e-07!503
|tf_chipseq_enrich=MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186385789915819!SMARCA4#6597;3:117.574427480916:1.03069197590886e-06:4.32828465106337e-05!SMARCB1#6598;3:13.6895368358681:0.000630578340937934:0.00518232383925219!SMARCC1#6599;3:32.7475194897236:4.71941722862287e-05:0.000824922537138316!SMARCC2#6601;3:70.6165308201732:4.74678670742709e-06:0.000147237795348078!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279808140388473
|tf_chipseq_enrich=MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186385789915819!SMARCA4#6597;3:117.574427480916:1.03069197590886e-06:4.32828465106337e-05!SMARCB1#6598;3:13.6895368358681:0.000630578340937934:0.00518232383925219!SMARCC1#6599;3:32.7475194897236:4.71941722862287e-05:0.000824922537138316!SMARCC2#6601;3:70.6165308201732:4.74678670742709e-06:0.000147237795348078!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279808140388473
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}}
}}

Revision as of 14:17, 19 October 2012


Full id: C2670_uterus_lung_cervix_adipose_penis_ductus_seminal



Phase1 CAGE Peaks

Hg19::chr2:173686542..173686585,+p5@RAPGEF4
Hg19::chr5:38557323..38557328,-p12@LIFR
Hg19::chr5:38557343..38557361,-p4@LIFR
Hg19::chr5:38557372..38557385,-p5@LIFR


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

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0004923leukemia inhibitory factor receptor activity0.0046508889673849
GO:0030552cAMP binding0.022470032592992
GO:0016208AMP binding0.022470032592992
GO:0005952cAMP-dependent protein kinase complex0.022470032592992
GO:0030551cyclic nucleotide binding0.022470032592992
GO:0008603cAMP-dependent protein kinase regulator activity0.022470032592992
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0457985933512357



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
endothelial cell of vascular tree5.68e-1024
Uber Anatomy
Ontology termp-valuen
adult organism8.90e-78114
neural tube1.12e-2256
neural rod1.12e-2256
future spinal cord1.12e-2256
neural keel1.12e-2256
anatomical cluster2.82e-21373
regional part of nervous system1.71e-2053
regional part of brain1.71e-2053
anatomical conduit3.71e-20240
regional part of forebrain3.49e-1941
forebrain3.49e-1941
anterior neural tube3.49e-1941
future forebrain3.49e-1941
telencephalon6.76e-1834
brain grey matter8.84e-1834
gray matter8.84e-1834
central nervous system1.16e-1781
neural plate2.89e-1782
presumptive neural plate2.89e-1782
neurectoderm9.15e-1786
nervous system1.60e-1689
cerebral hemisphere3.20e-1632
structure with developmental contribution from neural crest3.41e-16132
regional part of telencephalon3.99e-1632
tube7.16e-16192
brain2.71e-1568
future brain2.71e-1568
organ system subdivision1.49e-14223
pre-chordal neural plate2.89e-1261
ecto-epithelium6.87e-12104
regional part of cerebral cortex3.19e-1122
neocortex4.03e-1120
cerebral cortex1.47e-1025
pallium1.47e-1025
multi-tissue structure5.44e-10342
multi-cellular organism1.49e-09656
neural nucleus1.60e-099
nucleus of brain1.60e-099
ectoderm-derived structure7.06e-09171
ectoderm7.06e-09171
presumptive ectoderm7.06e-09171
epithelium3.06e-08306
anatomical system3.52e-08624
anatomical group4.11e-08625
cell layer5.64e-08309
telencephalic nucleus9.20e-087
basal ganglion1.33e-079
nuclear complex of neuraxis1.33e-079
aggregate regional part of brain1.33e-079
collection of basal ganglia1.33e-079
cerebral subcortex1.33e-079
compound organ1.98e-0768
embryo3.54e-07592
embryonic structure6.60e-07564
organ8.56e-07503


Overrepresented TFBS (DNA) motifs on this co-expression cluster<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}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
MXI1#460137.471178721569470.003741314738550960.0186385789915819
SMARCA4#65973117.5744274809161.03069197590886e-064.32828465106337e-05
SMARCB1#6598313.68953683586810.0006305783409379340.00518232383925219
SMARCC1#6599332.74751948972364.71941722862287e-050.000824922537138316
SMARCC2#6601370.61653082017324.74678670742709e-060.000147237795348078
ZNF263#1012736.166381227758010.006539814347975980.0279808140388473



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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