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Coexpression cluster:C2536: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2536_cervix_occipital_breast_parietal_uterus_smooth_temporal
|full_id=C2536_cervix_occipital_breast_parietal_uterus_smooth_temporal
|id=C2536
|id=C2536

Revision as of 15:17, 12 September 2012


Full id: C2536_cervix_occipital_breast_parietal_uterus_smooth_temporal



Phase1 CAGE Peaks

Hg19::chr1:164528340..164528379,+p4@PBX1
Hg19::chr1:164528384..164528409,+p3@PBX1
Hg19::chr1:164528410..164528428,+p1@PBX1
Hg19::chr1:164528445..164528459,+p2@PBX1


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 organism2.63e-39115
central nervous system9.45e-2782
regional part of nervous system5.01e-2594
nervous system5.01e-2594
neurectoderm4.18e-2390
ectoderm5.64e-23173
presumptive ectoderm5.64e-23173
neural plate7.74e-2386
presumptive neural plate7.74e-2386
brain9.15e-2369
future brain9.15e-2369
ectoderm-derived structure1.67e-22169
neural tube1.72e-2257
neural rod1.72e-2257
future spinal cord1.72e-2257
neural keel1.72e-2257
regional part of brain4.14e-2259
multi-tissue structure2.47e-21347
organism subdivision3.32e-21365
multi-cellular organism9.91e-20659
head1.29e-19123
anterior neural tube4.08e-1942
anterior region of body4.71e-19129
craniocervical region4.71e-19129
regional part of forebrain1.18e-1841
forebrain1.18e-1841
future forebrain1.18e-1841
pre-chordal neural plate4.14e-1861
telencephalon1.76e-1634
anatomical cluster2.05e-16286
cerebral hemisphere3.54e-1632
organ part4.33e-16219
regional part of telencephalon6.09e-1633
gray matter6.73e-1634
brain grey matter6.73e-1634
cerebral cortex5.79e-1425
pallium5.79e-1425
anatomical group6.95e-14626
anatomical system9.62e-14625
regional part of cerebral cortex2.11e-1322
organ2.51e-13511
embryo3.34e-13612
anatomical conduit3.70e-13241
cell layer8.61e-13312
neocortex1.44e-1220
epithelium1.44e-12309
embryonic structure6.82e-12605
developing anatomical structure6.82e-12605
germ layer1.61e-11604
embryonic tissue1.61e-11604
presumptive structure1.61e-11604
epiblast (generic)1.61e-11604
tube3.36e-11194
organ segment5.63e-0797


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#105147.971147625824820.0002476385788090830.00268178406597281
GATA2#2624412.7449317335543.78864877853583e-050.000722048703980846
GTF2F1#2962412.73966087675773.79492332235515e-050.000718524287279641
IRF1#365947.63716375356390.0002938853996185490.00307638541152266
MXI1#460149.96157162875930.0001015224754950450.00142435596698374
NFYA#4800418.42558069983058.67100748407158e-060.000234487661996104
NFYB#4801416.75979325353651.26678572070404e-050.000311444995020267
PBX3#5090421.91451268674414.33289161192893e-060.000136466485843862
RAD21#5885410.35503389545638.6948481184721e-050.00129430051688299
SP2#6668426.15353049384462.13562021071447e-067.74720525136537e-05
TAF1#687243.343046285745290.008005664898701650.0322384282381146
TAF7#687938.574802053692940.00250055433515240.0140353304782599
TBP#690843.706770687096390.005296377814784350.0244355878693406
ZNF263#1012748.221841637010680.0002187871180958320.00248963911819684



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.