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Coexpression cluster:C2443: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002049!5.18e-22!79;UBERON:0007798!5.18e-22!79;UBERON:0004535!8.20e-21!110;UBERON:0001009!3.50e-19!113;UBERON:0000914!2.97e-17!83;UBERON:0002329!2.97e-17!83;UBERON:0003077!2.97e-17!83;UBERON:0003059!2.97e-17!83;UBERON:0007282!2.97e-17!83;UBERON:0009618!2.97e-17!83;UBERON:0007285!2.97e-17!83;UBERON:0003081!3.86e-17!216;UBERON:0000486!7.11e-17!82;UBERON:0000055!9.94e-17!69;UBERON:0001981!2.50e-16!60;UBERON:0007500!2.50e-16!60;UBERON:0004537!2.50e-16!60;UBERON:0006965!2.50e-16!60;UBERON:0005256!4.65e-16!143;UBERON:0004290!2.04e-15!70;UBERON:0004872!2.99e-15!84;UBERON:0003914!2.12e-14!118;UBERON:0001637!4.03e-14!42;UBERON:0003509!4.03e-14!42;UBERON:0004572!4.03e-14!42;UBERON:0001134!1.39e-13!61;UBERON:0002036!1.39e-13!61;UBERON:0003082!1.39e-13!61;UBERON:0000926!2.11e-13!448;UBERON:0004120!2.11e-13!448;UBERON:0006603!2.11e-13!448;UBERON:0000490!5.52e-13!138;UBERON:0002385!8.64e-13!63;UBERON:0001015!8.64e-13!63;UBERON:0000383!8.64e-13!63;UBERON:0002204!3.06e-12!167;UBERON:0002100!6.51e-10!216;UBERON:0004573!7.61e-10!33;UBERON:0004571!7.61e-10!33;UBERON:0005085!6.66e-08!29;UBERON:0001986!1.21e-07!18;UBERON:0004638!1.21e-07!18;UBERON:0004852!1.21e-07!18;UBERON:0003102!3.41e-07!95;UBERON:0004211!3.52e-07!16;UBERON:0001285!3.52e-07!16;UBERON:0007684!3.52e-07!16;UBERON:0003220!3.52e-07!16;UBERON:0004208!3.52e-07!16;UBERON:0000487!3.84e-07!22;UBERON:0000353!6.70e-07!17;UBERON:0006914!7.24e-07!25
|ontology_enrichment_uberon=UBERON:0002049!5.18e-22!79;UBERON:0007798!5.18e-22!79;UBERON:0004535!8.20e-21!110;UBERON:0001009!3.50e-19!113;UBERON:0000914!2.97e-17!83;UBERON:0002329!2.97e-17!83;UBERON:0003077!2.97e-17!83;UBERON:0003059!2.97e-17!83;UBERON:0007282!2.97e-17!83;UBERON:0009618!2.97e-17!83;UBERON:0007285!2.97e-17!83;UBERON:0003081!3.86e-17!216;UBERON:0000486!7.11e-17!82;UBERON:0000055!9.94e-17!69;UBERON:0001981!2.50e-16!60;UBERON:0007500!2.50e-16!60;UBERON:0004537!2.50e-16!60;UBERON:0006965!2.50e-16!60;UBERON:0005256!4.65e-16!143;UBERON:0004290!2.04e-15!70;UBERON:0004872!2.99e-15!84;UBERON:0003914!2.12e-14!118;UBERON:0001637!4.03e-14!42;UBERON:0003509!4.03e-14!42;UBERON:0004572!4.03e-14!42;UBERON:0001134!1.39e-13!61;UBERON:0002036!1.39e-13!61;UBERON:0003082!1.39e-13!61;UBERON:0000926!2.11e-13!448;UBERON:0004120!2.11e-13!448;UBERON:0006603!2.11e-13!448;UBERON:0000490!5.52e-13!138;UBERON:0002385!8.64e-13!63;UBERON:0001015!8.64e-13!63;UBERON:0000383!8.64e-13!63;UBERON:0002204!3.06e-12!167;UBERON:0002100!6.51e-10!216;UBERON:0004573!7.61e-10!33;UBERON:0004571!7.61e-10!33;UBERON:0005085!6.66e-08!29;UBERON:0001986!1.21e-07!18;UBERON:0004638!1.21e-07!18;UBERON:0004852!1.21e-07!18;UBERON:0003102!3.41e-07!95;UBERON:0004211!3.52e-07!16;UBERON:0001285!3.52e-07!16;UBERON:0007684!3.52e-07!16;UBERON:0003220!3.52e-07!16;UBERON:0004208!3.52e-07!16;UBERON:0000487!3.84e-07!22;UBERON:0000353!6.70e-07!17;UBERON:0006914!7.24e-07!25
|pathway_enrichment=0.000145853209864357;0.0307750272813793;2;200;Focal adhesion (KEGG):04510!8.75676438203826e-05;0.0307750272813793;2;155;Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289!0.000128870835041632;0.0307750272813793;2;188;Focal Adhesion (Wikipathways):WP306
|pathway_enrichment=0.000145853209864357;0.0307750272813793;2;200;Focal adhesion (KEGG):04510!8.75676438203826e-05;0.0307750272813793;2;155;Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289!0.000128870835041632;0.0307750272813793;2;188;Focal Adhesion (Wikipathways):WP306
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}}
}}

Revision as of 11:38, 5 September 2012


Full id: C2443_Mesenchymal_Hepatic_Alveolar_Smooth_Astrocyte_Renal_Hair



Phase1 CAGE Peaks

Hg19::chr17:79479822..79479830,-p1@ACTG1
Hg19::chr19:1026566..1026648,+p1@CNN2
Hg19::chr19:2096259..2096342,-p1@MOB3A
Hg19::chr7:143078379..143078454,+p1@ZYX


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


p.valueFDRnGenesnPathwayName
0.0001458532098643570.03077502728137932200Focal adhesion (KEGG):04510
8.75676438203826e-050.03077502728137932155Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289
0.0001288708350416320.03077502728137932188Focal Adhesion (Wikipathways):WP306



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:0005911intercellular junction0.00105713136868672
GO:0030054cell junction0.00326156077542858
GO:0005913cell-cell adherens junction0.0104577467891468
GO:0031032actomyosin structure organization and biogenesis0.0126684703362576
GO:0005856cytoskeleton0.0142566507029949
GO:0005912adherens junction0.0217068263005428
GO:0044459plasma membrane part0.0264873599816309
GO:0043232intracellular non-membrane-bound organelle0.0336456441217229
GO:0043228non-membrane-bound organelle0.0336456441217229
GO:0005516calmodulin binding0.0339637806473224
GO:0005886plasma membrane0.0470180521288173
GO:0030036actin cytoskeleton organization and biogenesis0.048091021929576
GO:0030029actin filament-based process0.048091021929576



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
somatic cell7.07e-45591
animal cell5.15e-31679
eukaryotic cell5.15e-31679
native cell4.41e-26722
non-terminally differentiated cell1.83e-25180
mesodermal cell7.49e-24119
contractile cell1.26e-1859
embryonic cell3.39e-17248
muscle precursor cell2.74e-1657
myoblast2.74e-1657
multi-potent skeletal muscle stem cell2.74e-1657
muscle cell4.15e-1654
somatic stem cell4.93e-15436
smooth muscle cell6.02e-1542
smooth muscle myoblast6.02e-1542
multi fate stem cell7.10e-15430
stem cell3.68e-14444
electrically responsive cell2.30e-1360
electrically active cell2.30e-1360
fibroblast7.40e-1375
vascular associated smooth muscle cell6.71e-1232
meso-epithelial cell1.97e-0944
endothelial cell2.41e-0935
lining cell7.66e-0857
barrier cell7.66e-0857
blood vessel endothelial cell1.21e-0718
embryonic blood vessel endothelial progenitor cell1.21e-0718
endothelial cell of vascular tree1.82e-0724
epithelial cell of nephron3.52e-0716
Uber Anatomy
Ontology termp-valuen
vasculature5.18e-2279
vascular system5.18e-2279
cardiovascular system8.20e-21110
circulatory system3.50e-19113
somite2.97e-1783
paraxial mesoderm2.97e-1783
presomitic mesoderm2.97e-1783
presumptive segmental plate2.97e-1783
trunk paraxial mesoderm2.97e-1783
presumptive paraxial mesoderm2.97e-1783
lateral plate mesoderm3.86e-17216
multilaminar epithelium7.11e-1782
vessel9.94e-1769
blood vessel2.50e-1660
epithelial tube open at both ends2.50e-1660
blood vasculature2.50e-1660
vascular cord2.50e-1660
trunk mesenchyme4.65e-16143
dermomyotome2.04e-1570
splanchnic layer of lateral plate mesoderm2.99e-1584
epithelial tube2.12e-14118
artery4.03e-1442
arterial blood vessel4.03e-1442
arterial system4.03e-1442
skeletal muscle tissue1.39e-1361
striated muscle tissue1.39e-1361
myotome1.39e-1361
mesoderm2.11e-13448
mesoderm-derived structure2.11e-13448
presumptive mesoderm2.11e-13448
unilaminar epithelium5.52e-13138
muscle tissue8.64e-1363
musculature8.64e-1363
musculature of body8.64e-1363
musculoskeletal system3.06e-12167
trunk6.51e-10216
systemic artery7.61e-1033
systemic arterial system7.61e-1033
ectodermal placode6.66e-0829
endothelium1.21e-0718
blood vessel endothelium1.21e-0718
cardiovascular system endothelium1.21e-0718
surface structure3.41e-0795
nephron epithelium3.52e-0716
nephron3.52e-0716
uriniferous tubule3.52e-0716
metanephric mesenchyme3.52e-0716
nephrogenic mesenchyme3.52e-0716
simple squamous epithelium3.84e-0722
parenchyma6.70e-0717
squamous epithelium7.24e-0725


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
CCNT2#90546.336201576962630.0006203100587215640.00512090445204501
E2F6#187645.017155731697390.00157802193473060.00996776538292784
ELF1#199744.258097958807540.003041525565781240.016087814057464
EP300#203335.08045629466740.01144298405398240.0418904907853015
HEY1#2346244.040111043105710.00375304636917980.0186003136596958
HMGN3#932436.133910792512940.006640696683324720.0282942118517359
JUND#372735.245997956403270.01043432751748420.038687543723322
PAX5#507935.002174148383370.01196533174786410.0434917092686171
RXRA#6256315.055962854350.0004758307997303580.0043390633801658
SIN3A#2594245.408884726815140.001168172384885160.00796154761844302
SRF#6722310.34788369662590.001439893778401260.00923773366438045
TAF1#687243.343046285745290.008005664898701650.0322135864517627
TAF7#687938.574802053692940.00250055433515240.0140323139116104
TBP#690843.706770687096390.005296377814784350.0244140178575391
USF1#739134.771124457905970.01370465887188020.0483025400891027
ZBTB7A#5134147.35190930787590.000342223540015990.00346399343823706



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.