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Coexpression cluster:C3689: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.016737297989854!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156626071148283!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663607121119883!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276428780271197!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246284020162383!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329047570053041
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.016737297989854!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156626071148283!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663607121119883!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276428780271197!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246284020162383!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329047570053041
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}}
}}

Revision as of 16:17, 26 November 2012


Full id: C3689_brain_amygdala_temporal_duodenum_insula_putamen_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr17:7608489..7608500,+p3@EFNB3
Hg19::chr17:7608511..7608538,+p1@EFNB3
Hg19::chr17:7608540..7608553,+p2@EFNB3


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><br>

Cell Type
Ontology termp-valuen
neurectodermal cell6.47e-1359
ectodermal cell2.01e-1172
neural cell2.02e-0825
migratory neural crest cell5.98e-0841
Uber Anatomy
Ontology termp-valuen
central nervous system1.75e-2881
nervous system9.40e-2889
ectoderm-derived structure2.43e-26171
ectoderm2.43e-26171
presumptive ectoderm2.43e-26171
neurectoderm2.28e-2386
brain9.67e-2368
future brain9.67e-2368
neural plate2.09e-2182
presumptive neural plate2.09e-2182
regional part of nervous system2.69e-2053
regional part of brain2.69e-2053
neural tube3.16e-2056
neural rod3.16e-2056
future spinal cord3.16e-2056
neural keel3.16e-2056
ecto-epithelium1.41e-19104
cerebral hemisphere1.65e-1932
pre-chordal neural plate1.81e-1961
telencephalon6.98e-1934
regional part of forebrain1.97e-1841
forebrain1.97e-1841
anterior neural tube1.97e-1841
future forebrain1.97e-1841
brain grey matter2.30e-1834
gray matter2.30e-1834
regional part of telencephalon1.11e-1732
structure with developmental contribution from neural crest3.25e-17132
organ system subdivision1.72e-16223
anatomical cluster5.18e-16373
cerebral cortex1.50e-1525
pallium1.50e-1525
regional part of cerebral cortex5.51e-1522
cell layer9.16e-15309
epithelium2.76e-14306
neocortex8.95e-1420
multi-tissue structure1.46e-11342
organ part6.03e-11218
tube1.30e-10192
embryo1.58e-08592
multi-cellular organism3.93e-08656
anatomical conduit7.05e-08240
developing anatomical structure3.50e-07581


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)

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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
EP300#203336.77394172622320.003216880500103790.016737297989854
JUND#372736.994663941871030.002921845042734990.0156626071148283
RAD21#5885310.35503389545630.0009004912073565420.00663607121119883
SIN3A#2594235.408884726815140.006318961977991520.0276428780271197
SP1#666735.69838137814090.005403962701712170.0246284020162383
YY1#752834.911170749853860.008441455341808260.0329047570053041



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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