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Coexpression cluster:C4713: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4713_Neural_Macrophage_Neurons_Mast_medulloblastoma_brain_duodenum
|full_id=C4713_Neural_Macrophage_Neurons_Mast_medulloblastoma_brain_duodenum
|id=C4713
|id=C4713

Revision as of 17:50, 12 September 2012


Full id: C4713_Neural_Macrophage_Neurons_Mast_medulloblastoma_brain_duodenum



Phase1 CAGE Peaks

Hg19::chr8:101965104..101965119,-p6@YWHAZ
Hg19::chr8:101965124..101965140,-p7@YWHAZ
Hg19::chr8:101965146..101965236,-p5@YWHAZ


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
neurectodermal cell2.45e-1259
ectodermal cell3.29e-1271
neural cell8.71e-1125
migratory neural crest cell1.22e-0741
neuron associated cell8.65e-0717
neuron associated cell (sensu Vertebrata)8.65e-0717
Uber Anatomy
Ontology termp-valuen
ectoderm5.14e-17173
presumptive ectoderm5.14e-17173
ectoderm-derived structure1.54e-16169
regional part of nervous system1.40e-1394
nervous system1.40e-1394
central nervous system4.99e-1282
head9.64e-12123
anterior region of body7.65e-11129
craniocervical region7.65e-11129
cerebral hemisphere8.13e-1132
cerebral cortex5.37e-1025
pallium5.37e-1025
telencephalon8.43e-1034
regional part of telencephalon2.27e-0933
pre-chordal neural plate4.70e-0961
brain9.75e-0969
future brain9.75e-0969
gray matter1.02e-0834
brain grey matter1.02e-0834
regional part of cerebral cortex2.95e-0822
neocortex9.95e-0820
regional part of forebrain1.22e-0741
forebrain1.22e-0741
future forebrain1.22e-0741
neurectoderm1.49e-0790
neural plate3.57e-0786
presumptive neural plate3.57e-0786
anterior neural tube5.47e-0742
Disease
Ontology termp-valuen
disease of cellular proliferation1.45e-10239
cancer6.86e-10235
cell type cancer1.41e-08143


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
CCNT2#90536.336201576962630.003930750035764890.0191199107160938
E2F1#186934.907389214879320.008460985347239390.0327814530598136
EGR1#195834.988179094810140.008056488137383440.0322565292152651
ETS1#211339.728760922202340.001085840092584840.00765467792301503
MYC#460935.22228187160940.007020843755740150.0296130972499393
NFYA#4800318.42558069983050.0001598135507814160.00200249159328858
NFYB#4801316.75979325353650.0002123649923296180.00246736983356469
NRF1#4899312.21027944771090.0005492172401020010.0047357743840004
PAX5#507936.669565531177830.003370290999677260.0173702043878451
PBX3#5090321.91451268674419.49854535978121e-050.0013737966747406
SP1#666735.69838137814090.005403962701712170.0247928510193339
SP2#6668326.15353049384465.58768218891694e-050.000942613374460177
SRF#6722313.79717826216780.0003806615025800190.00376512043450654
TAF7#6879311.43306940492390.0006690181981945830.00545871809384719
ZBTB7A#5134137.35190930787590.002516255860282270.0140954326213269



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.