Personal tools

Coexpression cluster:C3084

From FANTOM5_SSTAR

Revision as of 15:56, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3084_Mallassezderived_Mesothelial_leiomyoma_granulosa_Sertoli_acute_Prostate



Phase1 CAGE Peaks

Hg19::chr11:114310081..114310082,+p6@REXO2
Hg19::chr11:114310102..114310118,+p3@REXO2
Hg19::chr11:114310124..114310140,+p4@REXO2


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
splanchnic layer of lateral plate mesoderm4.57e-1384
trunk7.79e-13216
mesenchyme8.65e-13238
entire embryonic mesenchyme8.65e-13238
trunk mesenchyme1.84e-12143
unilaminar epithelium1.90e-12138
vasculature1.53e-1179
vascular system1.53e-1179
multilaminar epithelium2.98e-1182
somite3.31e-1183
paraxial mesoderm3.31e-1183
presomitic mesoderm3.31e-1183
presumptive segmental plate3.31e-1183
trunk paraxial mesoderm3.31e-1183
presumptive paraxial mesoderm3.31e-1183
artery6.19e-1142
arterial blood vessel6.19e-1142
arterial system6.19e-1142
vessel8.51e-1169
dermomyotome9.32e-1170
epithelial tube1.01e-10118
blood vessel2.97e-1060
epithelial tube open at both ends2.97e-1060
blood vasculature2.97e-1060
vascular cord2.97e-1060
skeletal muscle tissue3.97e-1061
striated muscle tissue3.97e-1061
myotome3.97e-1061
muscle tissue2.38e-0963
musculature2.38e-0963
musculature of body2.38e-0963
primordium1.74e-08168
multi-tissue structure2.37e-08347
cell layer2.48e-08312
circulatory system2.91e-08113
cardiovascular system3.87e-08110
epithelium4.52e-08309
systemic artery6.43e-0833
systemic arterial system6.43e-0833
reproductive structure1.11e-0759
reproductive system1.11e-0759
organism subdivision3.00e-07365


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
ATF3#467322.46317452600878.81932387510763e-050.0012925643645697
CCNT2#90536.336201576962630.003930750035764890.0189137803725063
CTCF#1066435.360256373075030.0064925092527670.0278262957095262
CTCFL#140690319.74647435897440.0001298372005551160.00171083363471812
E2F4#1874312.66806031528440.0004917987006298980.00435426962488013
E2F6#187635.017155731697390.00791769806886330.0320423322592325
ELF1#199734.258097958807540.01295179875054610.0460077177547799
EP300#203336.77394172622320.003216880500103790.0166857602458575
ESR1#2099330.76860329615453.43136389821584e-050.000673624462717601
ETS1#211339.728760922202340.001085840092584840.00759877066667567
FOXA1#3169311.08141974938550.000734755275698670.00579410346109131
GATA3#2625327.2365163572064.94721007899563e-050.00084868868830523
HMGN3#932438.178547723350590.001827766942164210.0108294180332835
IRF1#365937.63716375356390.002244692747297240.0127610617731738
JUND#372736.994663941871030.002921845042734990.0156153195383379
MAX#414936.452555509007120.003721913834265510.0185747101322146
MXI1#460139.96157162875930.001011470541259020.0071817915465736
MYC#460935.22228187160940.007020843755740150.0293206134439278
NRF1#4899312.21027944771090.0005492172401020010.004694688110903
PAX5#507936.669565531177830.003370290999677260.0172282228826437
SIN3A#2594235.408884726815140.006318961977991520.027541360070923
SIX5#147912317.0867153554590.0002004060546325010.0023898387690984
SMARCC2#6601394.15537442689761.19621075407887e-064.84416653529441e-05
SMC3#9126315.04493284493280.0002935825420371870.00308031616514183
TCF12#6938310.63446490218640.0008313523990202070.00627715537892361
USF1#739136.361499277207960.00388404057290560.018951846075205
USF2#7392312.99219738506960.0004558979393427810.00420428475823583
ZNF143#7702313.50087655222790.0004062804962997170.00387679568323857



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.