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Coexpression cluster:C2633: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268289683944417!STAT1#6772;4:20.7065874971992:5.43610708103893e-06:0.000165474085525102!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123263955099155!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244561147138678!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.00032688220905188!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.001146792580103
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268289683944417!STAT1#6772;4:20.7065874971992:5.43610708103893e-06:0.000165474085525102!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123263955099155!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244561147138678!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.00032688220905188!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.001146792580103
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}}
}}

Revision as of 15:37, 26 November 2012


Full id: C2633_smallcell_Hep2_gall_cervical_splenic_mesothelioma_serous



Phase1 CAGE Peaks

Hg19::chr21:43816105..43816116,-p3@TMPRSS3
Hg19::chr21:43816124..43816151,-p2@TMPRSS3
Hg19::chr21:43816152..43816182,-p1@TMPRSS3
Hg19::chr21:43816226..43816231,-p4@TMPRSS3


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism3.56e-25114
regional part of nervous system1.03e-1853
regional part of brain1.03e-1853
larynx2.87e-179
neural tube2.95e-1756
neural rod2.95e-1756
future spinal cord2.95e-1756
neural keel2.95e-1756
brain grey matter6.26e-1734
gray matter6.26e-1734
regional part of forebrain5.30e-1641
forebrain5.30e-1641
anterior neural tube5.30e-1641
future forebrain5.30e-1641
telencephalon3.63e-1534
cerebral hemisphere6.39e-1532
regional part of telencephalon8.24e-1532
brain1.59e-1368
future brain1.59e-1368
neural nucleus1.60e-139
nucleus of brain1.60e-139
organ system subdivision1.09e-12223
basal ganglion5.40e-119
nuclear complex of neuraxis5.40e-119
aggregate regional part of brain5.40e-119
collection of basal ganglia5.40e-119
cerebral subcortex5.40e-119
telencephalic nucleus5.40e-117
neural plate6.94e-1182
presumptive neural plate6.94e-1182
pre-chordal neural plate1.60e-1061
central nervous system4.45e-1081
neurectoderm5.38e-1086
upper respiratory tract6.10e-1019
regional part of cerebral cortex3.18e-0922
multi-tissue structure5.50e-09342
neocortex9.57e-0920
organ part2.14e-08218
biliary system2.50e-089
biliary tree2.50e-089
biliary bud2.50e-089
nervous system2.59e-0889
cerebral cortex8.69e-0825
pallium8.69e-0825
foregut8.81e-0887
corpus striatum2.24e-074
striatum2.24e-074
ventral part of telencephalon2.24e-074
future corpus striatum2.24e-074
ecto-epithelium6.39e-07104
gyrus7.11e-076
brainstem9.58e-076
Disease
Ontology termp-valuen
carcinoma3.27e-18106
cell type cancer9.67e-12143
cancer1.42e-08235
disease of cellular proliferation4.18e-08239
adenocarcinoma5.87e-0825


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
CEBPB#105147.971147625824820.0002476385788090830.00268289683944417
STAT1#6772420.70658749719925.43610708103893e-060.000165474085525102
STAT3#6774410.51946499715428.16377768286615e-050.00123263955099155
TBP#690843.706770687096390.005296377814784350.0244561147138678
TFAP2A#7020416.5186343730451.34240829060362e-050.00032688220905188
TFAP2C#7022410.80922860986027.32289634782688e-050.001146792580103



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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