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Coexpression cluster:C3289: Difference between revisions

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|full_id=C3289_lung_Endothelial_Renal_Hepatic_Lymphatic_adipose_breast
|full_id=C3289_lung_Endothelial_Renal_Hepatic_Lymphatic_adipose_breast
|id=C3289
|id=C3289
|ontology_enrichment_celltype=CL:0000115!1.50e-25!35;CL:0002078!2.28e-20!44;CL:0002139!2.43e-20!24;CL:0000071!7.65e-16!18;CL:0002546!7.65e-16!18;CL:0000213!7.35e-13!57;CL:0000215!7.35e-13!57;CL:1000413!1.07e-08!9
|ontology_enrichment_celltype=CL:0000115!1.70e-34!36;CL:0002139!1.76e-32!24;CL:0002078!3.37e-25!45;CL:0000071!6.26e-25!18;CL:0002546!6.26e-25!18;CL:0000213!5.15e-17!58;CL:0000215!5.15e-17!58;CL:1000413!3.64e-13!9;CL:0002543!1.32e-09!6;CL:0002544!2.88e-09!6;CL:0005020!4.43e-09!6;CL:0002138!4.43e-09!6;CL:0005022!4.43e-09!6;CL:0000666!2.44e-08!5;CL:0002188!2.44e-08!5
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.56e-39!115;UBERON:0004111!1.76e-20!241;UBERON:0000025!1.65e-19!194;UBERON:0000477!1.68e-19!286;UBERON:0001049!6.36e-19!57;UBERON:0005068!6.36e-19!57;UBERON:0006241!6.36e-19!57;UBERON:0007135!6.36e-19!57;UBERON:0000955!1.91e-16!69;UBERON:0006238!1.91e-16!69;UBERON:0002616!1.96e-16!59;UBERON:0001017!4.45e-16!82;UBERON:0001986!7.65e-16!18;UBERON:0004638!7.65e-16!18;UBERON:0004852!7.65e-16!18;UBERON:0005743!3.02e-15!86;UBERON:0003080!1.10e-14!42;UBERON:0002780!5.00e-14!41;UBERON:0001890!5.00e-14!41;UBERON:0006240!5.00e-14!41;UBERON:0000073!2.61e-13!94;UBERON:0001016!2.61e-13!94;UBERON:0003075!4.50e-13!86;UBERON:0007284!4.50e-13!86;UBERON:0002020!8.70e-13!34;UBERON:0003528!8.70e-13!34;UBERON:0000468!1.64e-12!659;UBERON:0001893!2.37e-12!34;UBERON:0000467!2.65e-12!625;UBERON:0000480!3.80e-12!626;UBERON:0000487!4.02e-12!22;UBERON:0002346!5.83e-12!90;UBERON:0000055!6.52e-12!69;UBERON:0002791!6.61e-12!33;UBERON:0001869!1.79e-11!32;UBERON:0006914!2.50e-11!25;UBERON:0002049!1.04e-10!79;UBERON:0007798!1.04e-10!79;UBERON:0002619!1.86e-10!22;UBERON:0000119!6.47e-10!312;UBERON:0000483!1.27e-09!309;UBERON:0000922!1.88e-09!612;UBERON:0001950!2.95e-09!20;UBERON:0001009!4.96e-09!113;UBERON:0004872!7.10e-09!84;UBERON:0000153!9.56e-09!129;UBERON:0007811!9.56e-09!129;UBERON:0002050!9.88e-09!605;UBERON:0005423!9.88e-09!605;UBERON:0003915!1.07e-08!9;UBERON:0004700!1.07e-08!9;UBERON:0001917!1.07e-08!9;UBERON:0000923!1.98e-08!604;UBERON:0005291!1.98e-08!604;UBERON:0006598!1.98e-08!604;UBERON:0002532!1.98e-08!604;UBERON:0001981!2.07e-08!60;UBERON:0007500!2.07e-08!60;UBERON:0004537!2.07e-08!60;UBERON:0006965!2.07e-08!60;UBERON:0000956!2.89e-08!25;UBERON:0000203!2.89e-08!25;UBERON:0003056!3.09e-08!61;UBERON:0000033!3.99e-08!123;UBERON:0004535!4.11e-08!110;UBERON:0002465!5.21e-08!10;UBERON:0003914!3.77e-07!118;UBERON:0000062!4.06e-07!511;UBERON:0001473!5.04e-07!8;UBERON:0004536!5.04e-07!8;UBERON:0006558!5.04e-07!8;UBERON:0002298!6.94e-07!8
|ontology_enrichment_uberon=UBERON:0007023!9.75e-56!114;UBERON:0000477!3.64e-26!373;UBERON:0004111!4.27e-26!240;UBERON:0001049!1.26e-25!56;UBERON:0005068!1.26e-25!56;UBERON:0006241!1.26e-25!56;UBERON:0007135!1.26e-25!56;UBERON:0000025!4.71e-25!192;UBERON:0004638!6.26e-25!18;UBERON:0001986!6.26e-25!18;UBERON:0004852!6.26e-25!18;UBERON:0001017!4.22e-23!81;UBERON:0000073!4.42e-23!53;UBERON:0002616!4.42e-23!53;UBERON:0000955!7.39e-22!68;UBERON:0006238!7.39e-22!68;UBERON:0001016!1.35e-21!89;UBERON:0003528!2.94e-19!34;UBERON:0002020!2.94e-19!34;UBERON:0000487!3.52e-19!22;UBERON:0001893!1.21e-18!34;UBERON:0002780!2.84e-18!41;UBERON:0001890!2.84e-18!41;UBERON:0003080!2.84e-18!41;UBERON:0006240!2.84e-18!41;UBERON:0003075!5.78e-18!82;UBERON:0007284!5.78e-18!82;UBERON:0001869!3.35e-17!32;UBERON:0002791!3.84e-17!32;UBERON:0002346!1.64e-16!86;UBERON:0006914!4.22e-16!25;UBERON:0002619!3.40e-15!22;UBERON:0010314!4.06e-14!132;UBERON:0000055!2.97e-13!68;UBERON:0001950!3.44e-13!20;UBERON:0003915!3.64e-13!9;UBERON:0004700!3.64e-13!9;UBERON:0001917!3.64e-13!9;UBERON:0000119!5.78e-13!309;UBERON:0000956!8.84e-13!25;UBERON:0000203!8.84e-13!25;UBERON:0000483!2.30e-12!306;UBERON:0011216!9.23e-12!223;UBERON:0003056!1.22e-11!61;UBERON:0010371!1.81e-11!104;UBERON:0002049!5.47e-11!78;UBERON:0007798!5.47e-11!78;UBERON:0000468!8.29e-11!656;UBERON:0002465!1.67e-10!10;UBERON:0000467!5.06e-10!624;UBERON:0000480!6.05e-10!625;UBERON:0001009!8.15e-10!112;UBERON:0004872!6.01e-09!83;UBERON:0001473!9.31e-09!8;UBERON:0004536!9.31e-09!8;UBERON:0006558!9.31e-09!8;UBERON:0007500!9.55e-09!59;UBERON:0001981!9.55e-09!59;UBERON:0004537!9.55e-09!59;UBERON:0006965!9.55e-09!59;UBERON:0002298!1.26e-08!6;UBERON:0003076!1.46e-08!15;UBERON:0003057!1.46e-08!15;UBERON:0004535!1.96e-08!109;UBERON:0000125!3.17e-08!9;UBERON:0002308!3.17e-08!9;UBERON:0004121!3.32e-08!171;UBERON:0000924!3.32e-08!171;UBERON:0006601!3.32e-08!171;UBERON:0001638!7.59e-08!9;UBERON:0003920!7.59e-08!9;UBERON:0004582!7.59e-08!9;UBERON:0000922!8.61e-08!592;UBERON:0005423!2.44e-07!581;UBERON:0003914!2.81e-07!117;UBERON:0004732!3.89e-07!13;UBERON:0000200!4.65e-07!6;UBERON:0002050!9.29e-07!564
|tf_chipseq_enrich=GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436211228840003!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108888945127747!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109029390438214
|tf_chipseq_enrich=GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436211228840003!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108888945127747!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109029390438214
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}}
}}

Revision as of 14:58, 19 October 2012


Full id: C3289_lung_Endothelial_Renal_Hepatic_Lymphatic_adipose_breast



Phase1 CAGE Peaks

Hg19::chr12:52306161..52306194,+p3@ACVRL1
Hg19::chr12:52306196..52306215,+p6@ACVRL1
Hg19::chr12:52306220..52306231,+p9@ACVRL1


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


No GOStat results

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
adult organism9.75e-56114
anatomical cluster3.64e-26373
anatomical conduit4.27e-26240
neural tube1.26e-2556
neural rod1.26e-2556
future spinal cord1.26e-2556
neural keel1.26e-2556
tube4.71e-25192
blood vessel endothelium6.26e-2518
endothelium6.26e-2518
cardiovascular system endothelium6.26e-2518
central nervous system4.22e-2381
regional part of nervous system4.42e-2353
regional part of brain4.42e-2353
brain7.39e-2268
future brain7.39e-2268
nervous system1.35e-2189
brain grey matter2.94e-1934
gray matter2.94e-1934
simple squamous epithelium3.52e-1922
telencephalon1.21e-1834
regional part of forebrain2.84e-1841
forebrain2.84e-1841
anterior neural tube2.84e-1841
future forebrain2.84e-1841
neural plate5.78e-1882
presumptive neural plate5.78e-1882
cerebral hemisphere3.35e-1732
regional part of telencephalon3.84e-1732
neurectoderm1.64e-1686
squamous epithelium4.22e-1625
regional part of cerebral cortex3.40e-1522
structure with developmental contribution from neural crest4.06e-14132
vessel2.97e-1368
neocortex3.44e-1320
endothelial tube3.64e-139
arterial system endothelium3.64e-139
endothelium of artery3.64e-139
cell layer5.78e-13309
cerebral cortex8.84e-1325
pallium8.84e-1325
epithelium2.30e-12306
organ system subdivision9.23e-12223
pre-chordal neural plate1.22e-1161
ecto-epithelium1.81e-11104
vasculature5.47e-1178
vascular system5.47e-1178
multi-cellular organism8.29e-11656
lymphoid system1.67e-1010
anatomical system5.06e-10624
anatomical group6.05e-10625
circulatory system8.15e-10112
splanchnic layer of lateral plate mesoderm6.01e-0983
lymphatic vessel9.31e-098
lymph vasculature9.31e-098
lymphatic part of lymphoid system9.31e-098
epithelial tube open at both ends9.55e-0959
blood vessel9.55e-0959
blood vasculature9.55e-0959
vascular cord9.55e-0959
brainstem1.26e-086
posterior neural tube1.46e-0815
chordal neural plate1.46e-0815
cardiovascular system1.96e-08109
neural nucleus3.17e-089
nucleus of brain3.17e-089
ectoderm-derived structure3.32e-08171
ectoderm3.32e-08171
presumptive ectoderm3.32e-08171
vein7.59e-089
venous blood vessel7.59e-089
venous system7.59e-089
embryo8.61e-08592
developing anatomical structure2.44e-07581
epithelial tube2.81e-07117
segmental subdivision of nervous system3.89e-0713
gyrus4.65e-076
embryonic structure9.29e-07564


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
GATA2#2624312.7449317335540.0004829527704283790.00436211228840003
SPI1#668838.204323508522730.001810593189410520.0108888945127747
ZNF263#1012738.221841637010680.001799043925565870.0109029390438214



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.