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Coexpression cluster:C2919: Difference between revisions

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|tf_chipseq_enrich=TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323431834882791
|tf_chipseq_enrich=TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323431834882791
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}}
}}

Revision as of 15:48, 26 November 2012


Full id: C2919_smallcell_Smooth_skeletal_small_Urothelial_pituitary_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr8:139926246..139926269,-p2@COL22A1
Hg19::chr8:139926277..139926290,-p1@COL22A1
Hg19::chr8:139926293..139926315,-p3@COL22A1
Hg19::chr8:139926319..139926328,-p4@COL22A1


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>


Cell Type
Ontology termp-valuen
ectodermal cell9.90e-0972
oligodendrocyte1.36e-077
macroglial cell1.36e-077
astrocyte1.36e-077
oligodendrocyte precursor cell1.36e-077
embryonic cell1.44e-07250
Uber Anatomy
Ontology termp-valuen
epithelium4.91e-14306
cell layer1.47e-13309
anatomical cluster1.95e-13373
embryo2.52e-12592
anatomical conduit3.70e-12240
tube7.60e-12192
multi-cellular organism9.91e-12656
developing anatomical structure2.21e-10581
ecto-epithelium4.28e-10104
posterior neural tube9.00e-1015
chordal neural plate9.00e-1015
anatomical group9.26e-10625
anatomical system1.97e-09624
multi-tissue structure4.40e-09342
segmental subdivision of hindbrain3.41e-0812
hindbrain3.41e-0812
presumptive hindbrain3.41e-0812
embryonic structure4.02e-08564
structure with developmental contribution from neural crest4.98e-08132
neurectoderm6.32e-0886
ectoderm-derived structure8.56e-08171
ectoderm8.56e-08171
presumptive ectoderm8.56e-08171
neural plate1.23e-0782
presumptive neural plate1.23e-0782
segmental subdivision of nervous system2.65e-0713
germ layer3.20e-07560
germ layer / neural crest3.20e-07560
embryonic tissue3.20e-07560
presumptive structure3.20e-07560
germ layer / neural crest derived structure3.20e-07560
epiblast (generic)3.20e-07560
neural tube3.99e-0756
neural rod3.99e-0756
future spinal cord3.99e-0756
neural keel3.99e-0756
central nervous system4.30e-0781
systemic artery4.34e-0733
systemic arterial system4.34e-0733
nervous system4.50e-0789


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
TAF1#687243.343046285745290.008005664898701650.0323431834882791



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.