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Coexpression cluster:C4425

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Full id: C4425_Fibroblast_Preadipocyte_Ewing_mesodermal_Mesenchymal_Pancreatic_neurofibroma



Phase1 CAGE Peaks

Hg19::chr4:77870896..77870914,+p1@SEPT11
Hg19::chr4:77870934..77870956,+p3@SEPT11
Hg19::chr4:77870960..77871020,+p2@SEPT11


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
non-terminally differentiated cell6.23e-28180
fibroblast2.43e-1975
skin fibroblast7.13e-1223
fat cell2.02e-0815
Uber Anatomy
Ontology termp-valuen
organism subdivision8.28e-15365
somite4.93e-1283
paraxial mesoderm4.93e-1283
presomitic mesoderm4.93e-1283
presumptive segmental plate4.93e-1283
trunk paraxial mesoderm4.93e-1283
presumptive paraxial mesoderm4.93e-1283
integument8.87e-1145
integumental system8.87e-1145
central nervous system1.55e-1082
ectoderm-derived structure4.04e-10169
skin of body7.36e-1040
regional part of brain1.04e-0959
ectoderm1.12e-09173
presumptive ectoderm1.12e-09173
regional part of nervous system1.37e-0994
nervous system1.37e-0994
brain2.46e-0969
future brain2.46e-0969
cerebral hemisphere4.85e-0932
telencephalon1.48e-0834
head1.55e-08123
dermomyotome1.66e-0870
anterior neural tube2.08e-0842
surface structure2.14e-0895
regional part of telencephalon2.45e-0833
regional part of forebrain3.77e-0841
forebrain3.77e-0841
future forebrain3.77e-0841
gray matter3.86e-0834
brain grey matter3.86e-0834
cell layer4.88e-08312
neural tube6.77e-0857
neural rod6.77e-0857
future spinal cord6.77e-0857
neural keel6.77e-0857
epithelium1.68e-07309
cerebral cortex1.98e-0725
pallium1.98e-0725
multilaminar epithelium2.67e-0782
anterior region of body2.81e-07129
craniocervical region2.81e-07129
multi-cellular organism3.28e-07659


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#90536.336201576962630.003930750035764890.0190763756034038
E2F6#187635.017155731697390.00791769806886330.0323735061901113
EGR1#195834.988179094810140.008056488137383440.0321935860338303
ELF1#199734.258097958807540.01295179875054610.0464229840657658
EP300#203336.77394172622320.003216880500103790.0168084742120442
JUND#372736.994663941871030.002921845042734990.0157352949217862
MYC#460935.22228187160940.007020843755740150.029558185230207
NFKB1#479035.488063424193840.006049381815655430.0270470220234273
NRF1#4899312.21027944771090.0005492172401020010.00472757762622706
PAX5#507936.669565531177830.003370290999677260.0173470909129808
POU2F2#545239.106124057742520.001324165192682130.00884631795295394
RDBP#79363153.6384039900252.75057764221434e-071.40404486009396e-05
SIN3A#2594235.408884726815140.006318961977991520.0277825237862868
TCF12#6938310.63446490218640.0008313523990202070.00631137698635395
USF1#739136.361499277207960.00388404057290560.0190936838500206
YY1#752834.911170749853860.008441455341808260.0330689105192465
ZBTB7A#5134137.35190930787590.002516255860282270.0140705276967404
ZNF143#7702313.50087655222790.0004062804962997170.00390174977039504
ZNF263#1012738.221841637010680.001799043925565870.0109838856858514



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.