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Coexpression cluster:C4561: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281042472686092!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109999618606741
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281042472686092!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109999618606741
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}}
}}

Revision as of 16:49, 26 November 2012


Full id: C4561_mesenchymal_Preadipocyte_tenocyte_Fibroblast_Pancreatic_Neural_Smooth



Phase1 CAGE Peaks

Hg19::chr6:132722586..132722598,-p2@MOXD1
Hg19::chr6:132722599..132722600,-p3@MOXD1
Hg19::chr6:132722604..132722670,-p1@MOXD1


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>


Uber Anatomy
Ontology termp-valuen
multi-tissue structure7.08e-16342
dense mesenchyme tissue5.71e-1373
paraxial mesoderm9.38e-1372
presumptive paraxial mesoderm9.38e-1372
somite1.71e-1271
presomitic mesoderm1.71e-1271
presumptive segmental plate1.71e-1271
dermomyotome1.71e-1271
trunk paraxial mesoderm1.71e-1271
surface structure5.07e-1299
integument5.09e-1246
integumental system5.09e-1246
mesenchyme8.49e-12160
entire embryonic mesenchyme8.49e-12160
epithelial vesicle1.98e-1178
structure with developmental contribution from neural crest2.80e-11132
cerebral hemisphere7.17e-1132
multi-cellular organism1.76e-10656
muscle tissue2.35e-1064
musculature2.35e-1064
musculature of body2.35e-1064
skin of body2.41e-1041
ectoderm-derived structure2.65e-10171
ectoderm2.65e-10171
presumptive ectoderm2.65e-10171
telencephalon2.71e-1034
skeletal muscle tissue5.76e-1062
striated muscle tissue5.76e-1062
myotome5.76e-1062
multilaminar epithelium5.76e-1083
regional part of telencephalon8.15e-1032
cerebral cortex8.60e-1025
pallium8.60e-1025
anatomical system1.01e-09624
anatomical group1.54e-09625
anatomical cluster3.05e-09373
pre-chordal neural plate3.10e-0961
regional part of forebrain5.10e-0941
forebrain5.10e-0941
anterior neural tube5.10e-0941
future forebrain5.10e-0941
brain grey matter6.58e-0934
gray matter6.58e-0934
tissue1.10e-08773
trunk mesenchyme1.21e-08122
epithelium3.28e-08306
regional part of cerebral cortex5.10e-0822
organism subdivision5.45e-08264
organ part5.70e-08218
cell layer8.34e-08309
central nervous system2.02e-0781
neocortex2.23e-0720
neural plate4.11e-0782
presumptive neural plate4.11e-0782
organ component layer4.38e-0766


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
CTCF#1066435.360256373075030.0064925092527670.0281042472686092
ZNF263#1012738.221841637010680.001799043925565870.0109999618606741



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.