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Coexpression cluster:C4817: Difference between revisions

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|full_id=C4817_normal_lung_Endothelial_spleen_Lymphatic_heart_adipose
|full_id=C4817_normal_lung_Endothelial_spleen_Lymphatic_heart_adipose
|id=C4817
|id=C4817
|ontology_enrichment_celltype=CL:0002139!3.78e-18!24;CL:0000222!2.41e-16!119;CL:0000115!1.11e-14!35;CL:0000071!1.22e-13!18;CL:0002546!1.22e-13!18;CL:0000359!6.42e-12!32;CL:0000187!2.46e-11!54;CL:0000192!6.50e-11!42;CL:0000514!6.50e-11!42;CL:0000183!9.80e-11!59;CL:0002078!1.22e-10!44;CL:0000680!2.43e-10!57;CL:0000056!2.43e-10!57;CL:0000355!2.43e-10!57;CL:0000393!4.48e-10!60;CL:0000211!4.48e-10!60;CL:0000213!2.34e-08!57;CL:0000215!2.34e-08!57;CL:1000413!8.80e-08!9
|ontology_enrichment_celltype=CL:0002139!7.68e-22!24;CL:0000115!2.16e-19!36;CL:0000071!2.07e-16!18;CL:0002546!2.07e-16!18;CL:0000222!1.18e-14!121;CL:0002078!1.38e-13!45;CL:0000213!1.95e-10!58;CL:0000215!1.95e-10!58;CL:0000359!2.03e-10!32;CL:1000413!2.58e-09!9;CL:0000192!5.34e-08!43;CL:0000514!5.34e-08!43;CL:0000187!9.37e-08!55;CL:0005020!5.43e-07!6;CL:0002138!5.43e-07!6;CL:0005022!5.43e-07!6;CL:0000680!7.81e-07!58;CL:0000056!7.81e-07!58;CL:0000355!7.81e-07!58
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!3.44e-36!84;UBERON:0007023!5.37e-34!115;UBERON:0004111!2.83e-33!241;UBERON:0000025!3.20e-33!194;UBERON:0000055!6.66e-33!69;UBERON:0002049!7.34e-31!79;UBERON:0007798!7.34e-31!79;UBERON:0001981!1.29e-30!60;UBERON:0007500!1.29e-30!60;UBERON:0004537!1.29e-30!60;UBERON:0006965!1.29e-30!60;UBERON:0001009!2.09e-29!113;UBERON:0000477!4.27e-29!286;UBERON:0004535!7.52e-28!110;UBERON:0003914!1.30e-24!118;UBERON:0000119!2.29e-24!312;UBERON:0000483!4.75e-24!309;UBERON:0001637!1.05e-19!42;UBERON:0003509!1.05e-19!42;UBERON:0004572!1.05e-19!42;UBERON:0000490!7.12e-17!138;UBERON:0004573!1.84e-15!33;UBERON:0004571!1.84e-15!33;UBERON:0001986!1.22e-13!18;UBERON:0004638!1.22e-13!18;UBERON:0004852!1.22e-13!18;UBERON:0002385!1.04e-12!63;UBERON:0001015!1.04e-12!63;UBERON:0000383!1.04e-12!63;UBERON:0001049!1.14e-12!57;UBERON:0005068!1.14e-12!57;UBERON:0006241!1.14e-12!57;UBERON:0007135!1.14e-12!57;UBERON:0002616!3.16e-12!59;UBERON:0000468!3.60e-12!659;UBERON:0007100!4.50e-12!27;UBERON:0001134!5.45e-12!61;UBERON:0002036!5.45e-12!61;UBERON:0003082!5.45e-12!61;UBERON:0000480!7.06e-12!626;UBERON:0003080!7.98e-12!42;UBERON:0000467!8.29e-12!625;UBERON:0003075!1.16e-11!86;UBERON:0007284!1.16e-11!86;UBERON:0002780!3.04e-11!41;UBERON:0001890!3.04e-11!41;UBERON:0006240!3.04e-11!41;UBERON:0000481!3.21e-11!347;UBERON:0000487!6.74e-11!22;UBERON:0000948!1.44e-10!24;UBERON:0005498!1.44e-10!24;UBERON:0004140!1.44e-10!24;UBERON:0009881!1.44e-10!24;UBERON:0004141!1.44e-10!24;UBERON:0003084!1.44e-10!24;UBERON:0007005!1.44e-10!24;UBERON:0004139!1.44e-10!24;UBERON:0004291!1.44e-10!24;UBERON:0000947!1.88e-10!21;UBERON:0010191!1.88e-10!21;UBERON:0002346!3.66e-10!90;UBERON:0000475!4.78e-10!365;UBERON:0006914!5.59e-10!25;UBERON:0004290!7.91e-10!70;UBERON:0001017!8.56e-10!82;UBERON:0000955!1.00e-09!69;UBERON:0006238!1.00e-09!69;UBERON:0005743!1.68e-09!86;UBERON:0002020!4.42e-09!34;UBERON:0003528!4.42e-09!34;UBERON:0001893!5.27e-09!34;UBERON:0002791!9.31e-09!33;UBERON:0001869!2.17e-08!32;UBERON:0003056!6.45e-08!61;UBERON:0000073!8.28e-08!94;UBERON:0001016!8.28e-08!94;UBERON:0003915!8.80e-08!9;UBERON:0004700!8.80e-08!9;UBERON:0001917!8.80e-08!9;UBERON:0003103!2.06e-07!69;UBERON:0002619!2.37e-07!22;UBERON:0000486!3.17e-07!82;UBERON:0005256!3.35e-07!143;UBERON:0000914!6.33e-07!83;UBERON:0002329!6.33e-07!83;UBERON:0003077!6.33e-07!83;UBERON:0003059!6.33e-07!83;UBERON:0007282!6.33e-07!83;UBERON:0009618!6.33e-07!83;UBERON:0007285!6.33e-07!83;UBERON:0001950!9.00e-07!20
|ontology_enrichment_uberon=UBERON:0007023!1.08e-43!114;UBERON:0004111!4.67e-40!240;UBERON:0000025!8.23e-39!192;UBERON:0004872!4.95e-36!83;UBERON:0000055!1.48e-33!68;UBERON:0007500!6.36e-31!59;UBERON:0001981!6.36e-31!59;UBERON:0004537!6.36e-31!59;UBERON:0006965!6.36e-31!59;UBERON:0000477!1.64e-30!373;UBERON:0002049!1.68e-28!78;UBERON:0007798!1.68e-28!78;UBERON:0001009!7.46e-27!112;UBERON:0003914!1.55e-26!117;UBERON:0004535!4.69e-25!109;UBERON:0000119!1.06e-23!309;UBERON:0000483!1.57e-23!306;UBERON:0001637!7.81e-19!42;UBERON:0003509!7.81e-19!42;UBERON:0004572!7.81e-19!42;UBERON:0000481!1.85e-16!342;UBERON:0004638!2.07e-16!18;UBERON:0001986!2.07e-16!18;UBERON:0004852!2.07e-16!18;UBERON:0004573!3.16e-15!33;UBERON:0004571!3.16e-15!33;UBERON:0001049!7.35e-15!56;UBERON:0005068!7.35e-15!56;UBERON:0006241!7.35e-15!56;UBERON:0007135!7.35e-15!56;UBERON:0000073!1.10e-14!53;UBERON:0002616!1.10e-14!53;UBERON:0000490!6.11e-14!148;UBERON:0002780!1.42e-13!41;UBERON:0001890!1.42e-13!41;UBERON:0003080!1.42e-13!41;UBERON:0006240!1.42e-13!41;UBERON:0000487!1.46e-13!22;UBERON:0010314!8.12e-13!132;UBERON:0000468!1.23e-12!656;UBERON:0000467!5.70e-12!624;UBERON:0000480!7.69e-12!625;UBERON:0007100!1.49e-11!27;UBERON:0000955!1.52e-11!68;UBERON:0006238!1.52e-11!68;UBERON:0003075!5.30e-11!82;UBERON:0007284!5.30e-11!82;UBERON:0006914!6.01e-11!25;UBERON:0003528!8.01e-11!34;UBERON:0002020!8.01e-11!34;UBERON:0001893!9.27e-11!34;UBERON:0002050!2.16e-10!564;UBERON:0000923!2.21e-10!560;UBERON:0010316!2.21e-10!560;UBERON:0005291!2.21e-10!560;UBERON:0006598!2.21e-10!560;UBERON:0010317!2.21e-10!560;UBERON:0002532!2.21e-10!560;UBERON:0002791!5.68e-10!32;UBERON:0001017!6.75e-10!81;UBERON:0001869!7.01e-10!32;UBERON:0002346!9.13e-10!86;UBERON:0000948!1.04e-09!24;UBERON:0005498!1.04e-09!24;UBERON:0004140!1.04e-09!24;UBERON:0009881!1.04e-09!24;UBERON:0004141!1.04e-09!24;UBERON:0003084!1.04e-09!24;UBERON:0007005!1.04e-09!24;UBERON:0004139!1.04e-09!24;UBERON:0004291!1.04e-09!24;UBERON:0000947!1.18e-09!21;UBERON:0010191!1.18e-09!21;UBERON:0005423!2.33e-09!581;UBERON:0003915!2.58e-09!9;UBERON:0004700!2.58e-09!9;UBERON:0001917!2.58e-09!9;UBERON:0000922!2.72e-09!592;UBERON:0005256!2.85e-09!122;UBERON:0002385!2.96e-09!64;UBERON:0001015!2.96e-09!64;UBERON:0000383!2.96e-09!64;UBERON:0002619!3.23e-09!22;UBERON:0001016!1.75e-08!89;UBERON:0001134!1.89e-08!62;UBERON:0002036!1.89e-08!62;UBERON:0003082!1.89e-08!62;UBERON:0001950!2.22e-08!20;UBERON:0003056!7.91e-08!61;UBERON:0003103!1.68e-07!68;UBERON:0011216!2.02e-07!223;UBERON:0000956!2.13e-07!25;UBERON:0000203!2.13e-07!25;UBERON:0007503!3.24e-07!78;UBERON:0001638!4.57e-07!9;UBERON:0003920!4.57e-07!9;UBERON:0004582!4.57e-07!9;UBERON:0003104!9.19e-07!160;UBERON:0009142!9.19e-07!160
|tf_chipseq_enrich=GATA2#2624;3:12.744931733554:0.000482952770428379:0.00439403296373983
|tf_chipseq_enrich=GATA2#2624;3:12.744931733554:0.000482952770428379:0.00439403296373983
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}}
}}

Revision as of 16:16, 19 October 2012


Full id: C4817_normal_lung_Endothelial_spleen_Lymphatic_heart_adipose



Phase1 CAGE Peaks

Hg19::chr9:27109392..27109435,+p1@TEK
Hg19::chr9:27109440..27109456,+p2@TEK
Hg19::chr9:27109469..27109474,+p6@TEK


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 organism1.08e-43114
anatomical conduit4.67e-40240
tube8.23e-39192
splanchnic layer of lateral plate mesoderm4.95e-3683
vessel1.48e-3368
epithelial tube open at both ends6.36e-3159
blood vessel6.36e-3159
blood vasculature6.36e-3159
vascular cord6.36e-3159
anatomical cluster1.64e-30373
vasculature1.68e-2878
vascular system1.68e-2878
circulatory system7.46e-27112
epithelial tube1.55e-26117
cardiovascular system4.69e-25109
cell layer1.06e-23309
epithelium1.57e-23306
artery7.81e-1942
arterial blood vessel7.81e-1942
arterial system7.81e-1942
multi-tissue structure1.85e-16342
blood vessel endothelium2.07e-1618
endothelium2.07e-1618
cardiovascular system endothelium2.07e-1618
systemic artery3.16e-1533
systemic arterial system3.16e-1533
neural tube7.35e-1556
neural rod7.35e-1556
future spinal cord7.35e-1556
neural keel7.35e-1556
regional part of nervous system1.10e-1453
regional part of brain1.10e-1453
unilaminar epithelium6.11e-14148
regional part of forebrain1.42e-1341
forebrain1.42e-1341
anterior neural tube1.42e-1341
future forebrain1.42e-1341
simple squamous epithelium1.46e-1322
structure with developmental contribution from neural crest8.12e-13132
multi-cellular organism1.23e-12656
anatomical system5.70e-12624
anatomical group7.69e-12625
primary circulatory organ1.49e-1127
brain1.52e-1168
future brain1.52e-1168
neural plate5.30e-1182
presumptive neural plate5.30e-1182
squamous epithelium6.01e-1125
brain grey matter8.01e-1134
gray matter8.01e-1134
telencephalon9.27e-1134
embryonic structure2.16e-10564
germ layer2.21e-10560
germ layer / neural crest2.21e-10560
embryonic tissue2.21e-10560
presumptive structure2.21e-10560
germ layer / neural crest derived structure2.21e-10560
epiblast (generic)2.21e-10560
regional part of telencephalon5.68e-1032
central nervous system6.75e-1081
cerebral hemisphere7.01e-1032
neurectoderm9.13e-1086
heart1.04e-0924
primitive heart tube1.04e-0924
primary heart field1.04e-0924
anterior lateral plate mesoderm1.04e-0924
heart tube1.04e-0924
heart primordium1.04e-0924
cardiac mesoderm1.04e-0924
cardiogenic plate1.04e-0924
heart rudiment1.04e-0924
aorta1.18e-0921
aortic system1.18e-0921
developing anatomical structure2.33e-09581
endothelial tube2.58e-099
arterial system endothelium2.58e-099
endothelium of artery2.58e-099
embryo2.72e-09592
trunk mesenchyme2.85e-09122
muscle tissue2.96e-0964
musculature2.96e-0964


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#2624312.7449317335540.0004829527704283790.00439403296373983



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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