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Coexpression cluster:C4023: Difference between revisions

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|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321112683501961!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128252894488198!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277183447444015!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329823103046432
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321112683501961!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128252894488198!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277183447444015!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329823103046432
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}}
}}

Revision as of 16:30, 26 November 2012


Full id: C4023_Mesenchymal_heart_skeletal_left_tongue_temporal_brain



Phase1 CAGE Peaks

Hg19::chr20:32031426..32031441,-p3@SNTA1
Hg19::chr20:32031457..32031576,-p1@SNTA1
Hg19::chr20:32031680..32031703,-p2@SNTA1


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
fat cell4.80e-0915
Uber Anatomy
Ontology termp-valuen
adult organism5.78e-27114
structure with developmental contribution from neural crest9.74e-25132
neural tube2.27e-2256
neural rod2.27e-2256
future spinal cord2.27e-2256
neural keel2.27e-2256
neural plate5.79e-2282
presumptive neural plate5.79e-2282
brain1.86e-2168
future brain1.86e-2168
central nervous system3.72e-2181
regional part of nervous system5.33e-2153
regional part of brain5.33e-2153
multi-tissue structure2.35e-20342
neurectoderm4.44e-2086
epithelium6.79e-19306
nervous system1.17e-1889
cell layer1.54e-18309
anatomical cluster6.13e-18373
ecto-epithelium1.75e-17104
anatomical conduit1.81e-16240
regional part of forebrain4.13e-1641
forebrain4.13e-1641
anterior neural tube4.13e-1641
future forebrain4.13e-1641
ectoderm-derived structure6.04e-16171
ectoderm6.04e-16171
presumptive ectoderm6.04e-16171
telencephalon8.07e-1634
brain grey matter9.30e-1634
gray matter9.30e-1634
tube2.50e-15192
cerebral hemisphere8.94e-1532
regional part of telencephalon1.07e-1432
pre-chordal neural plate1.09e-1361
regional part of cerebral cortex4.32e-1122
cerebral cortex6.54e-1125
pallium6.54e-1125
neocortex5.37e-1020
organ part1.20e-09218
organ system subdivision1.22e-09223
multi-cellular organism1.70e-09656
compound organ4.71e-0968
organism subdivision7.77e-09264
organ2.16e-08503
mesenchyme3.33e-08160
entire embryonic mesenchyme3.33e-08160
anatomical system3.62e-08624
anatomical group5.88e-08625
posterior neural tube1.63e-0715
chordal neural plate1.63e-0715
dense mesenchyme tissue4.52e-0773
trunk mesenchyme4.78e-07122
paraxial mesoderm8.56e-0772
presumptive paraxial mesoderm8.56e-0772
primary circulatory organ8.93e-0727


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
EGR1#195834.988179094810140.008056488137383440.0321112683501961
IRF1#365937.63716375356390.002244692747297240.0128252894488198
SIN3A#2594235.408884726815140.006318961977991520.0277183447444015
YY1#752834.911170749853860.008441455341808260.0329823103046432



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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