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Coexpression cluster:C4380: Difference between revisions

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|tf_chipseq_enrich=TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630908394137999
|tf_chipseq_enrich=TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630908394137999
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}}
}}

Revision as of 16:42, 26 November 2012


Full id: C4380_retina_smallcell_acute_rectum_penis_lung_temporal



Phase1 CAGE Peaks

Hg19::chr4:156587853..156587884,+p5@GUCY1A3
Hg19::chr4:156587946..156587975,+p2@GUCY1A3
Hg19::chr4:156587979..156588015,+p1@GUCY1A3


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism6.43e-71114
neural tube3.53e-3156
neural rod3.53e-3156
future spinal cord3.53e-3156
neural keel3.53e-3156
regional part of nervous system1.18e-2853
regional part of brain1.18e-2853
neural plate4.75e-2682
presumptive neural plate4.75e-2682
regional part of forebrain2.02e-2541
forebrain2.02e-2541
anterior neural tube2.02e-2541
future forebrain2.02e-2541
neurectoderm9.30e-2486
brain5.33e-2268
future brain5.33e-2268
central nervous system5.92e-2281
telencephalon2.02e-2134
nervous system2.94e-2189
brain grey matter4.89e-2134
gray matter4.89e-2134
cerebral hemisphere3.69e-2032
regional part of telencephalon6.08e-2032
pre-chordal neural plate9.76e-2061
ecto-epithelium3.35e-19104
regional part of cerebral cortex2.24e-1722
organ system subdivision2.29e-17223
neocortex7.87e-1620
structure with developmental contribution from neural crest1.41e-15132
cerebral cortex1.87e-1525
pallium1.87e-1525
ectoderm-derived structure3.83e-13171
ectoderm3.83e-13171
presumptive ectoderm3.83e-13171
anatomical cluster4.66e-12373
multi-tissue structure2.36e-09342
organ part2.23e-08218
organ2.78e-08503
anatomical conduit6.57e-08240
basal ganglion1.48e-079
nuclear complex of neuraxis1.48e-079
aggregate regional part of brain1.48e-079
collection of basal ganglia1.48e-079
cerebral subcortex1.48e-079
tube3.60e-07192
posterior neural tube4.35e-0715
chordal neural plate4.35e-0715
neural nucleus4.67e-079
nucleus of brain4.67e-079
temporal lobe7.01e-076


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
TCF12#6938310.63446490218640.0008313523990202070.00630908394137999



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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