Coexpression cluster:C424: Difference between revisions
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|tf_chipseq_enrich=STAT3#6774;7:3.06817729083665:0.00565146722640425:0.0255236145149593 | |tf_chipseq_enrich=STAT3#6774;7:3.06817729083665:0.00565146722640425:0.0255236145149593 | ||
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}} | }} | ||
Revision as of 14:12, 26 November 2012
Full id: C424_Hepatocyte_liver_Synoviocyte_tenocyte_Fibroblast_Adipocyte_Cardiac
Phase1 CAGE Peaks
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.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 5.39695550498319e-08 | 1.13875761155145e-05 | 3 | 69 | Complement and coagulation cascades (KEGG):04610 |
| 2.26219774485948e-05 | 0.00286394234499211 | 2 | 56 | Staphylococcus aureus infection (KEGG):05150 |
| 0.000138328844145387 | 0.0145936930573384 | 2 | 138 | Systemic lupus erythematosus (KEGG):05322 |
| 2.79572408770279e-06 | 0.000442423336878966 | 2 | 20 | Complement Activation, Classical Pathway (Wikipathways):WP545 |
| 2.27747619344567e-08 | 7.20821215225554e-06 | 3 | 52 | Complement and Coagulation Cascades (Wikipathways):WP558 |
| 1.78259609854325e-08 | 7.20821215225554e-06 | 3 | 48 | {FCGR2B,50} (Static Module):NA |
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 ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0006508 | proteolysis | 0.0132525917284209 |
| GO:0004252 | serine-type endopeptidase activity | 0.0132525917284209 |
| GO:0008236 | serine-type peptidase activity | 0.0132525917284209 |
| GO:0017171 | serine hydrolase activity | 0.0132525917284209 |
| GO:0004175 | endopeptidase activity | 0.033273032044513 |
| GO:0006958 | complement activation, classical pathway | 0.033273032044513 |
| GO:0002455 | humoral immune response mediated by circulating immunoglobulin | 0.033273032044513 |
| GO:0006956 | complement activation | 0.033273032044513 |
| GO:0002541 | activation of plasma proteins during acute inflammatory response | 0.033273032044513 |
| GO:0016064 | immunoglobulin mediated immune response | 0.033273032044513 |
| GO:0019724 | B cell mediated immunity | 0.033273032044513 |
| GO:0008233 | peptidase activity | 0.033273032044513 |
| GO:0002253 | activation of immune response | 0.033273032044513 |
| GO:0002449 | lymphocyte mediated immunity | 0.033273032044513 |
| GO:0006959 | humoral immune response | 0.033273032044513 |
| GO:0002460 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 0.033273032044513 |
| GO:0002250 | adaptive immune response | 0.033273032044513 |
| GO:0002443 | leukocyte mediated immunity | 0.033273032044513 |
| GO:0002526 | acute inflammatory response | 0.033273032044513 |
| GO:0050778 | positive regulation of immune response | 0.033273032044513 |
| GO:0002684 | positive regulation of immune system process | 0.033273032044513 |
| GO:0050776 | regulation of immune response | 0.033273032044513 |
| GO:0007596 | blood coagulation | 0.033273032044513 |
| GO:0002682 | regulation of immune system process | 0.033273032044513 |
| GO:0050817 | coagulation | 0.033273032044513 |
| GO:0007599 | hemostasis | 0.033273032044513 |
| GO:0051240 | positive regulation of multicellular organismal process | 0.033273032044513 |
| GO:0002252 | immune effector process | 0.033605128731863 |
| GO:0045087 | innate immune response | 0.0336202558677497 |
| GO:0050878 | regulation of body fluid levels | 0.0355140395553653 |
| GO:0042060 | wound healing | 0.0355140395553653 |
| GO:0044267 | cellular protein metabolic process | 0.0355140395553653 |
| GO:0044260 | cellular macromolecule metabolic process | 0.0357225886968076 |
| GO:0019538 | protein metabolic process | 0.0379340249739084 |
| GO:0008015 | blood circulation | 0.0379340249739084 |
| GO:0003013 | circulatory system process | 0.0379340249739084 |
| GO:0004867 | serine-type endopeptidase inhibitor activity | 0.0387405217571341 |
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>
| Ontology term | p-value | n |
|---|---|---|
| fibroblast | 4.85e-14 | 76 |
| muscle precursor cell | 1.19e-08 | 58 |
| myoblast | 1.19e-08 | 58 |
| multi-potent skeletal muscle stem cell | 1.19e-08 | 58 |
| muscle cell | 5.60e-08 | 55 |
| contractile cell | 6.95e-08 | 59 |
| preadipocyte | 9.21e-07 | 12 |
| Ontology term | p-value | n |
|---|---|---|
| trunk mesenchyme | 5.56e-11 | 122 |
| mesenchyme | 1.47e-10 | 160 |
| entire embryonic mesenchyme | 1.47e-10 | 160 |
| muscle tissue | 5.53e-10 | 64 |
| musculature | 5.53e-10 | 64 |
| musculature of body | 5.53e-10 | 64 |
| skeletal muscle tissue | 3.27e-09 | 62 |
| striated muscle tissue | 3.27e-09 | 62 |
| myotome | 3.27e-09 | 62 |
| primary circulatory organ | 4.13e-09 | 27 |
| trunk | 6.16e-09 | 199 |
| organism subdivision | 2.31e-08 | 264 |
| heart | 2.71e-08 | 24 |
| primitive heart tube | 2.71e-08 | 24 |
| primary heart field | 2.71e-08 | 24 |
| anterior lateral plate mesoderm | 2.71e-08 | 24 |
| heart tube | 2.71e-08 | 24 |
| heart primordium | 2.71e-08 | 24 |
| cardiac mesoderm | 2.71e-08 | 24 |
| cardiogenic plate | 2.71e-08 | 24 |
| heart rudiment | 2.71e-08 | 24 |
| dense mesenchyme tissue | 9.44e-08 | 73 |
| somite | 1.43e-07 | 71 |
| presomitic mesoderm | 1.43e-07 | 71 |
| presumptive segmental plate | 1.43e-07 | 71 |
| dermomyotome | 1.43e-07 | 71 |
| trunk paraxial mesoderm | 1.43e-07 | 71 |
| paraxial mesoderm | 2.67e-07 | 72 |
| presumptive paraxial mesoderm | 2.67e-07 | 72 |
| multi-tissue structure | 5.72e-07 | 342 |
| adult organism | 8.15e-07 | 114 |
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 | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| STAT3#6774 | 7 | 3.06817729083665 | 0.00565146722640425 | 0.0255236145149593 |
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.
