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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2012_mature_lung_adipose_medulla_breast_vagina_penis
|full_id=C2012_mature_lung_adipose_medulla_breast_vagina_penis
|id=C2012
|id=C2012

Revision as of 14:40, 12 September 2012


Full id: C2012_mature_lung_adipose_medulla_breast_vagina_penis



Phase1 CAGE Peaks

Hg19::chr8:38585834..38585867,+p6@TACC1
Hg19::chr8:38585882..38585897,+p12@TACC1
Hg19::chr8:38585926..38585943,+p16@TACC1
Hg19::chr8:38585964..38585975,+p19@TACC1
Hg19::chr8:38586002..38586022,+p8@TACC1


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
fat cell3.73e-0715
Uber Anatomy
Ontology termp-valuen
adult organism2.88e-58115
neural tube1.66e-2557
neural rod1.66e-2557
future spinal cord1.66e-2557
neural keel1.66e-2557
regional part of brain3.41e-2459
anterior neural tube5.62e-2142
regional part of forebrain3.86e-2041
forebrain3.86e-2041
future forebrain3.86e-2041
neural plate1.03e-1986
presumptive neural plate1.03e-1986
brain4.31e-1969
future brain4.31e-1969
neurectoderm2.60e-1890
central nervous system9.17e-1882
gray matter1.68e-1634
brain grey matter1.68e-1634
telencephalon2.07e-1634
regional part of telencephalon6.65e-1633
anatomical cluster1.60e-15286
regional part of nervous system2.25e-1594
nervous system2.25e-1594
cerebral hemisphere2.61e-1532
anterior region of body5.57e-15129
craniocervical region5.57e-15129
anatomical conduit1.92e-14241
head5.02e-14123
organism subdivision2.02e-13365
pre-chordal neural plate3.42e-1361
regional part of cerebral cortex2.49e-1222
cerebral cortex2.13e-1125
pallium2.13e-1125
ectoderm-derived structure2.53e-11169
neocortex2.82e-1120
tube4.17e-11194
multi-tissue structure4.50e-11347
ectoderm9.24e-11173
presumptive ectoderm9.24e-11173
multi-cellular organism2.23e-09659
organ6.89e-09511
epithelium1.52e-08309
cell layer2.40e-08312
organ part2.98e-08219
anatomical system4.37e-07625
anatomical group5.62e-07626
brainstem8.21e-078


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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