Coexpression cluster:C15: Difference between revisions
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|pathway_enrichment=5.88831399165079e-05;0.0372730275671495;3;37;Sandbox Pathway (Wikipathways):WP4 | |pathway_enrichment=5.88831399165079e-05;0.0372730275671495;3;37;Sandbox Pathway (Wikipathways):WP4 | ||
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| |||
}} | }} | ||
Revision as of 17:28, 8 August 2012
Full id: C15_anaplastic_small_skeletal_neuroblastoma_parietal_temporal_tongue
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 |
|---|---|---|---|---|
| 5.88831399165079e-05 | 0.0372730275671495 | 3 | 37 | Sandbox Pathway (Wikipathways):WP4 |
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:0032501 | multicellular organismal process | 5.00634533324367e-06 |
| GO:0005886 | plasma membrane | 3.42875078428577e-05 |
| GO:0007267 | cell-cell signaling | 0.00366776085921252 |
| GO:0004115 | 3',5'-cyclic-AMP phosphodiesterase activity | 0.00366776085921252 |
| GO:0007275 | multicellular organismal development | 0.00366776085921252 |
| GO:0048731 | system development | 0.00366776085921252 |
| GO:0009888 | tissue development | 0.00366776085921252 |
| GO:0048856 | anatomical structure development | 0.00366776085921252 |
| GO:0016020 | membrane | 0.00366776085921252 |
| GO:0007492 | endoderm development | 0.00366776085921252 |
| GO:0007154 | cell communication | 0.00366776085921252 |
| GO:0032502 | developmental process | 0.00432462599023232 |
| GO:0048513 | organ development | 0.00588213876947777 |
| GO:0022405 | hair cycle process | 0.00867634199135259 |
| GO:0042633 | hair cycle | 0.00867634199135259 |
| GO:0022404 | molting cycle process | 0.00867634199135259 |
| GO:0001942 | hair follicle development | 0.00867634199135259 |
| GO:0042303 | molting cycle | 0.00867634199135259 |
| GO:0005626 | insoluble fraction | 0.0101898653964574 |
| GO:0009653 | anatomical structure morphogenesis | 0.013993170901665 |
| GO:0048869 | cellular developmental process | 0.0160576500520975 |
| GO:0030154 | cell differentiation | 0.0160576500520975 |
| GO:0007268 | synaptic transmission | 0.0160576500520975 |
| GO:0030326 | embryonic limb morphogenesis | 0.0212811527743405 |
| GO:0035113 | embryonic appendage morphogenesis | 0.0212811527743405 |
| GO:0019226 | transmission of nerve impulse | 0.0220754966944497 |
| GO:0048736 | appendage development | 0.0220754966944497 |
| GO:0060173 | limb development | 0.0220754966944497 |
| GO:0035107 | appendage morphogenesis | 0.0220754966944497 |
| GO:0035108 | limb morphogenesis | 0.0220754966944497 |
| GO:0035103 | sterol regulatory element binding protein cleavage | 0.0220754966944497 |
| GO:0031628 | opioid receptor binding | 0.0220754966944497 |
| GO:0031852 | mu-type opioid receptor binding | 0.0220754966944497 |
| GO:0006992 | sterol depletion response, sterol regulatory element binding protein cleavage | 0.0220754966944497 |
| GO:0001621 | platelet ADP receptor activity | 0.0220754966944497 |
| GO:0022834 | ligand-gated channel activity | 0.0220754966944497 |
| GO:0015276 | ligand-gated ion channel activity | 0.0220754966944497 |
| GO:0009887 | organ morphogenesis | 0.0220754966944497 |
| GO:0001608 | nucleotide receptor activity, G-protein coupled | 0.0224816909284426 |
| GO:0045028 | purinergic nucleotide receptor activity, G-protein coupled | 0.0224816909284426 |
| GO:0016502 | nucleotide receptor activity | 0.0224816909284426 |
| GO:0001614 | purinergic nucleotide receptor activity | 0.0224816909284426 |
| GO:0004114 | 3',5'-cyclic-nucleotide phosphodiesterase activity | 0.0229604318474109 |
| GO:0004112 | cyclic-nucleotide phosphodiesterase activity | 0.0244590058623249 |
| GO:0030967 | ER-nuclear sterol response pathway | 0.0311486706709485 |
| GO:0016889 | endodeoxyribonuclease activity, producing 3'-phosphomonoesters | 0.0311486706709485 |
| GO:0016921 | pyroglutamyl-peptidase II activity | 0.0311486706709485 |
| GO:0004531 | deoxyribonuclease II activity | 0.0311486706709485 |
| GO:0042599 | lamellar body | 0.0311486706709485 |
| GO:0006587 | serotonin biosynthetic process from tryptophan | 0.0311486706709485 |
| GO:0007399 | nervous system development | 0.0311486706709485 |
| GO:0030182 | neuron differentiation | 0.0322492956070361 |
| GO:0005625 | soluble fraction | 0.0410661040884613 |
| GO:0042808 | neuronal Cdc2-like kinase binding | 0.0410661040884613 |
| GO:0032933 | SREBP-mediated signaling pathway | 0.0410661040884613 |
| GO:0035315 | hair cell differentiation | 0.0410661040884613 |
| GO:0006991 | response to sterol depletion | 0.0410661040884613 |
| GO:0048699 | generation of neurons | 0.0430163327849991 |
| GO:0044425 | membrane part | 0.0455971486067447 |
| GO:0022836 | gated channel activity | 0.0458670234766792 |
| GO:0044464 | cell part | 0.0458670234766792 |
| GO:0022008 | neurogenesis | 0.0458670234766792 |
| GO:0004931 | ATP-gated cation channel activity | 0.0458670234766792 |
| GO:0042428 | serotonin metabolic process | 0.0458670234766792 |
| GO:0007431 | salivary gland development | 0.0458670234766792 |
| GO:0004791 | thioredoxin-disulfide reductase activity | 0.0458670234766792 |
| GO:0016920 | pyroglutamyl-peptidase activity | 0.0458670234766792 |
| GO:0042427 | serotonin biosynthetic process | 0.0458670234766792 |
| GO:0007188 | G-protein signaling, coupled to cAMP nucleotide second messenger | 0.0487235021259181 |
| GO:0045177 | apical part of cell | 0.0499502093922339 |
| GO:0019933 | cAMP-mediated signaling | 0.0499502093922339 |
| GO:0043565 | sequence-specific DNA binding | 0.0499502093922339 |
| GO:0048468 | cell development | 0.0499502093922339 |
| GO:0042640 | anagen | 0.0499502093922339 |
| GO:0045669 | positive regulation of osteoblast differentiation | 0.0499502093922339 |
| GO:0006911 | phagocytosis, engulfment | 0.0499502093922339 |
| GO:0004510 | tryptophan 5-monooxygenase activity | 0.0499502093922339 |
| GO:0000305 | response to oxygen radical | 0.0499502093922339 |
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><br>uberon_data<br>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| cell type cancer | 3.15e-19 | 143 |
| cancer | 1.57e-13 | 235 |
| carcinoma | 3.76e-13 | 106 |
| disease of cellular proliferation | 6.13e-13 | 239 |
| germ cell and embryonal cancer | 3.39e-07 | 22 |
| germ cell cancer | 3.39e-07 | 22 |
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) |
|---|---|
|
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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
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