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Coexpression cluster:C2966: Difference between revisions

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|tf_chipseq_enrich=SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245245930823498
|tf_chipseq_enrich=SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245245930823498
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}}
}}

Revision as of 15:50, 26 November 2012


Full id: C2966_cervix_acute_smooth_penis_rectum_uterus_lung



Phase1 CAGE Peaks

Hg19::chr10:100995586..100995597,-p4@HPSE2
Hg19::chr10:100995603..100995614,-p2@HPSE2
Hg19::chr10:100995626..100995635,-p5@HPSE2


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 organism1.83e-42114
neural tube3.99e-2856
neural rod3.99e-2856
future spinal cord3.99e-2856
neural keel3.99e-2856
regional part of nervous system6.49e-2553
regional part of brain6.49e-2553
brain1.21e-1968
future brain1.21e-1968
central nervous system6.58e-1981
neural plate2.67e-1782
presumptive neural plate2.67e-1782
nervous system2.04e-1689
neurectoderm3.24e-1686
posterior neural tube4.11e-1615
chordal neural plate4.11e-1615
regional part of forebrain5.15e-1541
forebrain5.15e-1541
anterior neural tube5.15e-1541
future forebrain5.15e-1541
organ system subdivision6.23e-15223
brain grey matter2.55e-1434
gray matter2.55e-1434
telencephalon5.02e-1434
brainstem7.48e-146
segmental subdivision of hindbrain1.54e-1212
hindbrain1.54e-1212
presumptive hindbrain1.54e-1212
ecto-epithelium2.21e-12104
segmental subdivision of nervous system1.71e-1113
pons5.49e-113
regional part of telencephalon6.87e-1132
cerebral hemisphere8.08e-1132
structure with developmental contribution from neural crest2.04e-10132
neocortex4.14e-1020
neural nucleus3.88e-099
nucleus of brain3.88e-099
regional part of cerebral cortex4.29e-0922
anatomical conduit4.46e-09240
regional part of metencephalon4.86e-099
metencephalon4.86e-099
future metencephalon4.86e-099
pre-chordal neural plate5.42e-0961
anatomical cluster1.30e-08373
intestine1.75e-0817
gyrus2.29e-086
locus ceruleus6.13e-082
brainstem nucleus6.13e-082
hindbrain nucleus6.13e-082
cerebral cortex7.24e-0825
pallium7.24e-0825
multi-tissue structure8.73e-08342
ectoderm-derived structure3.24e-07171
ectoderm3.24e-07171
presumptive ectoderm3.24e-07171
small intestine9.29e-074


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
SP1#666735.69838137814090.005403962701712170.0245245930823498



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.