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Coexpression cluster:C3978: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3978_smallcell_somatostatinoma_small_merkel_Hep2_carcinoid_gastrointestinal
|full_id=C3978_smallcell_somatostatinoma_small_merkel_Hep2_carcinoid_gastrointestinal
|id=C3978
|id=C3978

Revision as of 16:59, 12 September 2012


Full id: C3978_smallcell_somatostatinoma_small_merkel_Hep2_carcinoid_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr1:38259459..38259532,+p2@MANEAL
Hg19::chr1:38259540..38259569,+p3@MANEAL
Hg19::chr1:38259727..38259807,+p1@MANEAL


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell1.11e-08254
Uber Anatomy
Ontology termp-valuen
central nervous system8.83e-1782
regional part of nervous system3.25e-1594
nervous system3.25e-1594
neural tube8.85e-1457
neural rod8.85e-1457
future spinal cord8.85e-1457
neural keel8.85e-1457
brain1.20e-1369
future brain1.20e-1369
adult organism6.47e-13115
regional part of forebrain1.72e-1141
forebrain1.72e-1141
future forebrain1.72e-1141
anterior neural tube2.46e-1142
regional part of brain2.64e-1059
telencephalon5.76e-0934
gray matter8.70e-0934
brain grey matter8.70e-0934
cerebral hemisphere9.94e-0932
regional part of telencephalon1.36e-0833
subdivision of digestive tract2.01e-08129
endodermal part of digestive tract2.01e-08129
neurectoderm2.23e-0890
regional part of cerebral cortex2.69e-0822
neural plate2.83e-0886
presumptive neural plate2.83e-0886
neocortex6.10e-0820
foregut7.75e-0898
ectoderm1.80e-07173
presumptive ectoderm1.80e-07173
larynx1.84e-079
ectoderm-derived structure2.61e-07169
digestive system3.50e-07155
digestive tract3.50e-07155
primitive gut3.50e-07155
Disease
Ontology termp-valuen
cancer6.46e-43235
disease of cellular proliferation1.78e-41239
cell type cancer2.26e-34143
carcinoma1.11e-31106
organ system cancer1.10e-16137
disease of anatomical entity1.42e-0739
adenocarcinoma1.70e-0725
hematologic cancer6.46e-0751
immune system cancer6.46e-0751


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
E2F1#186934.907389214879320.008460985347239390.0325700065858367
E2F6#187635.017155731697390.00791769806886330.0322598396057431
ELF1#199734.258097958807540.01295179875054610.0462784532385057
ESR1#2099220.51240219743630.003099741577095180.0163131222257618
GABPB1#255337.067683836182170.002832212825417420.015425191660084
MYC#460935.22228187160940.007020843755740150.0294833092483211
REST#597839.650028716128020.001112636247114590.00768281765371244
SUZ12#23512350.11578091106297.93834897779404e-060.000222689559197376
USF1#739136.361499277207960.00388404057290560.0190497470364275
ZNF263#1012738.221841637010680.001799043925565870.0109531507836175



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.