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Coexpression cluster:C4364

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Full id: C4364_astrocytoma_Fibroblast_Smooth_Olfactory_sacrococcigeal_normal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr4:119274062..119274072,-p5@PRSS12
Hg19::chr4:119274086..119274113,-p4@PRSS12
Hg19::chr4:119274121..119274219,-p1@PRSS12


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
surface structure1.23e-2199
organism subdivision1.05e-17264
multilaminar epithelium9.69e-1683
dense mesenchyme tissue1.71e-1473
somite3.33e-1471
presomitic mesoderm3.33e-1471
presumptive segmental plate3.33e-1471
dermomyotome3.33e-1471
trunk paraxial mesoderm3.33e-1471
paraxial mesoderm6.20e-1472
presumptive paraxial mesoderm6.20e-1472
multi-tissue structure1.79e-12342
epithelial vesicle2.60e-1278
skin of body3.67e-1241
multi-cellular organism7.71e-12656
skeletal muscle tissue1.15e-1162
striated muscle tissue1.15e-1162
myotome1.15e-1162
subdivision of head2.05e-1149
muscle tissue2.10e-1164
musculature2.10e-1164
musculature of body2.10e-1164
head4.61e-1156
integument7.61e-1146
integumental system7.61e-1146
anatomical system2.66e-10624
anatomical group4.20e-10625
trunk mesenchyme6.59e-10122
anterior region of body1.19e-0962
craniocervical region1.19e-0962
endoderm-derived structure1.81e-09160
endoderm1.81e-09160
presumptive endoderm1.81e-09160
trunk3.49e-09199
anatomical cluster1.63e-08373
mesenchyme3.18e-08160
entire embryonic mesenchyme3.18e-08160
mouth3.54e-0829
stomodeum3.54e-0829
unilaminar epithelium4.04e-08148
digestive system1.16e-07145
digestive tract1.16e-07145
primitive gut1.16e-07145
artery4.52e-0742
arterial blood vessel4.52e-0742
arterial system4.52e-0742
epithelium5.27e-07306
systemic artery5.32e-0733
systemic arterial system5.32e-0733
ectodermal placode5.98e-0731
cell layer6.06e-07309
orifice6.16e-0736


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285359285133755
CTCF#1066435.360256373075030.0064925092527670.0280623752783071
CTCFL#140690319.74647435897440.0001298372005551160.00172169469131232
E2F6#187635.017155731697390.00791769806886330.0323608370294687
EBF1#187938.9064668465690.00141523283560980.00917818567550002
RAD21#5885310.35503389545630.0009004912073565420.00666712045974123
SMC3#9126315.04493284493280.0002935825420371870.0031021314354332
USF1#739136.361499277207960.00388404057290560.019090089575683
YY1#752834.911170749853860.008441455341808260.0330565112277133
ZNF143#7702313.50087655222790.0004062804962997170.00390103233916026



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.