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Coexpression cluster:C3013: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!6.16e-09!14
|ontology_enrichment_disease=DOID:2394!6.16e-09!14
|ontology_enrichment_uberon=UBERON:0000914!2.82e-17!83;UBERON:0002329!2.82e-17!83;UBERON:0003077!2.82e-17!83;UBERON:0003059!2.82e-17!83;UBERON:0007282!2.82e-17!83;UBERON:0009618!2.82e-17!83;UBERON:0007285!2.82e-17!83;UBERON:0000468!2.57e-16!659;UBERON:0005256!7.34e-15!143;UBERON:0000467!9.19e-15!625;UBERON:0000480!2.12e-14!626;UBERON:0002100!2.57e-14!216;UBERON:0000486!4.04e-14!82;UBERON:0004290!5.28e-14!70;UBERON:0004872!1.71e-13!84;UBERON:0002385!4.66e-13!63;UBERON:0001015!4.66e-13!63;UBERON:0000383!4.66e-13!63;UBERON:0001134!4.84e-13!61;UBERON:0002036!4.84e-13!61;UBERON:0003082!4.84e-13!61;UBERON:0000926!5.98e-12!448;UBERON:0004120!5.98e-12!448;UBERON:0006603!5.98e-12!448;UBERON:0003102!7.14e-12!95;UBERON:0000490!4.55e-11!138;UBERON:0002049!6.20e-11!79;UBERON:0007798!6.20e-11!79;UBERON:0003104!8.70e-11!238;UBERON:0009142!8.70e-11!238;UBERON:0003914!1.61e-10!118;UBERON:0001637!1.91e-10!42;UBERON:0003509!1.91e-10!42;UBERON:0004572!1.91e-10!42;UBERON:0001981!2.27e-10!60;UBERON:0007500!2.27e-10!60;UBERON:0004537!2.27e-10!60;UBERON:0006965!2.27e-10!60;UBERON:0000475!2.60e-10!365;UBERON:0000055!2.12e-09!69;UBERON:0004573!3.73e-09!33;UBERON:0004571!3.73e-09!33;UBERON:0001009!5.00e-09!113;UBERON:0004535!6.84e-09!110;UBERON:0002199!1.24e-08!45;UBERON:0002416!1.24e-08!45;UBERON:0002050!2.59e-08!605;UBERON:0005423!2.59e-08!605;UBERON:0000922!3.45e-08!612;UBERON:0000923!4.14e-08!604;UBERON:0005291!4.14e-08!604;UBERON:0006598!4.14e-08!604;UBERON:0002532!4.14e-08!604;UBERON:0000481!6.31e-08!347;UBERON:0000948!8.12e-08!24;UBERON:0005498!8.12e-08!24;UBERON:0004140!8.12e-08!24;UBERON:0009881!8.12e-08!24;UBERON:0004141!8.12e-08!24;UBERON:0003084!8.12e-08!24;UBERON:0007005!8.12e-08!24;UBERON:0004139!8.12e-08!24;UBERON:0004291!8.12e-08!24;UBERON:0002097!8.27e-08!40;UBERON:0007100!1.13e-07!27
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}}
}}

Revision as of 18:50, 8 August 2012


Full id: C3013_Smooth_Fibroblast_hepatic_mesenchymal_basal_spindle_Mesothelial



Phase1 CAGE Peaks

Hg19::chr10:33247124..33247207,-p1@ITGB1
Hg19::chr10:33247223..33247234,-p3@ITGB1
Hg19::chr8:62627160..62627178,-p2@ASPH


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:0031594neuromuscular junction0.0291501513585371
GO:0004597peptide-aspartate beta-dioxygenase activity0.0291501513585371
GO:0042383sarcolemma0.0291501513585371
GO:0008307structural constituent of muscle0.0291501513585371
GO:0001726ruffle0.0291501513585371
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0.0291501513585371
GO:0030176integral to endoplasmic reticulum membrane0.0291501513585371
GO:0008305integrin complex0.0291501513585371
GO:0031227intrinsic to endoplasmic reticulum membrane0.0291501513585371
GO:0031252leading edge0.0291501513585371
GO:0006968cellular defense response0.0291501513585371
GO:0051213dioxygenase activity0.0291501513585371
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0291501513585371
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0291501513585371
GO:0048770pigment granule0.0291501513585371
GO:0042470melanosome0.0291501513585371
GO:0007229integrin-mediated signaling pathway0.0291501513585371
GO:0007160cell-matrix adhesion0.0301724825008919
GO:0031589cell-substrate adhesion0.0301724825008919
GO:0046982protein heterodimerization activity0.0301724825008919
GO:0043235receptor complex0.0301724825008919
GO:0018193peptidyl-amino acid modification0.0316759691239406
GO:0031301integral to organelle membrane0.0347967680636087
GO:0031300intrinsic to organelle membrane0.0364586862712288
GO:0003012muscle system process0.0365254835953352
GO:0006936muscle contraction0.0365254835953352
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0377240214046705
GO:0007156homophilic cell adhesion0.0423186472106859
GO:0032501multicellular organismal process0.0427628214148144
GO:0016477cell migration0.0446564411088571
GO:0009055electron carrier activity0.046911570277405



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
somite2.82e-1783
paraxial mesoderm2.82e-1783
presomitic mesoderm2.82e-1783
presumptive segmental plate2.82e-1783
trunk paraxial mesoderm2.82e-1783
presumptive paraxial mesoderm2.82e-1783
multi-cellular organism2.57e-16659
trunk mesenchyme7.34e-15143
anatomical system9.19e-15625
anatomical group2.12e-14626
trunk2.57e-14216
multilaminar epithelium4.04e-1482
dermomyotome5.28e-1470
splanchnic layer of lateral plate mesoderm1.71e-1384
muscle tissue4.66e-1363
musculature4.66e-1363
musculature of body4.66e-1363
skeletal muscle tissue4.84e-1361
striated muscle tissue4.84e-1361
myotome4.84e-1361
mesoderm5.98e-12448
mesoderm-derived structure5.98e-12448
presumptive mesoderm5.98e-12448
surface structure7.14e-1295
unilaminar epithelium4.55e-11138
vasculature6.20e-1179
vascular system6.20e-1179
mesenchyme8.70e-11238
entire embryonic mesenchyme8.70e-11238
epithelial tube1.61e-10118
artery1.91e-1042
arterial blood vessel1.91e-1042
arterial system1.91e-1042
blood vessel2.27e-1060
epithelial tube open at both ends2.27e-1060
blood vasculature2.27e-1060
vascular cord2.27e-1060
organism subdivision2.60e-10365
vessel2.12e-0969
systemic artery3.73e-0933
systemic arterial system3.73e-0933
circulatory system5.00e-09113
cardiovascular system6.84e-09110
integument1.24e-0845
integumental system1.24e-0845
embryonic structure2.59e-08605
developing anatomical structure2.59e-08605
embryo3.45e-08612
germ layer4.14e-08604
embryonic tissue4.14e-08604
presumptive structure4.14e-08604
epiblast (generic)4.14e-08604
multi-tissue structure6.31e-08347
heart8.12e-0824
primitive heart tube8.12e-0824
primary heart field8.12e-0824
anterior lateral plate mesoderm8.12e-0824
heart tube8.12e-0824
heart primordium8.12e-0824
cardiac mesoderm8.12e-0824
cardiogenic plate8.12e-0824
heart rudiment8.12e-0824
skin of body8.27e-0840
primary circulatory organ1.13e-0727
Disease
Ontology termp-valuen
ovarian cancer6.16e-0914


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

No analysis results for this cluster

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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