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Coexpression cluster:C4622

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Full id: C4622_cervical_liver_glassy_Prostate_Hep2_Small_epitheloid



Phase1 CAGE Peaks

Hg19::chr6:64282377..64282392,+p2@PTP4A1
Hg19::chr6:64282416..64282440,+p3@PTP4A1
Hg19::chr6:64282447..64282471,+p1@PTP4A1


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>disease_data<br>


Cell Type
Ontology termp-valuen
endodermal cell5.22e-0759
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.93e-09169
endoderm1.93e-09169
presumptive endoderm1.93e-09169
digestive system9.30e-08155
digestive tract9.30e-08155
primitive gut9.30e-08155
larynx1.51e-079
subdivision of digestive tract2.99e-07129
endodermal part of digestive tract2.99e-07129
exocrine gland9.44e-0731
exocrine system9.44e-0731
Disease
Ontology termp-valuen
carcinoma6.38e-08106


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#90536.336201576962630.003930750035764890.0191065625516731
CEBPB#105137.971147625824820.001974187055288560.011575461591471
E2F1#186934.907389214879320.008460985347239390.0327510784878372
E2F6#187635.017155731697390.00791769806886330.0324153848927485
EGR1#195834.988179094810140.008056488137383440.0322342858897517
ELF1#199734.258097958807540.01295179875054610.0464740228718575
EP300#203336.77394172622320.003216880500103790.0168337399814781
ETS1#211339.728760922202340.001085840092584840.0076500305875248
FOS#235338.99795530889440.001372499272417130.00901524852276557
FOSL2#2355316.93020060456170.0002060162053171620.00244002341427978
GATA1#2623313.56030814380040.0004009615963782630.00389327149164647
HMGN3#932438.178547723350590.001827766942164210.0109148694420887
IRF1#365937.63716375356390.002244692747297240.0128689392235262
JUN#3725312.51282919233630.0005103313992726250.00446273976460133
MXI1#460139.96157162875930.001011470541259020.00723095159549257
MYC#460935.22228187160940.007020843755740150.0295915856574416
NANOG#79923329.24477848101273.99627955670032e-050.000740801279059683
NFKB1#479035.488063424193840.006049381815655430.0270794816958226
NFYA#4800318.42558069983050.0001598135507814160.00200177109979136
NFYB#4801316.75979325353650.0002123649923296180.00246599815809573
PAX5#507936.669565531177830.003370290999677260.0173633495321277
POU2F2#545239.106124057742520.001324165192682130.008855381222932
RFX5#5993312.04791082719510.0005717246050312580.00486716221265565
SIN3A#2594235.408884726815140.006318961977991520.0278164834570898
SP1#666735.69838137814090.005403962701712170.024779788400251
SP2#6668326.15353049384465.58768218891694e-050.000942156829396667
SREBF1#6720347.00584944048839.62099323994382e-060.000255351185002921
TAF7#6879311.43306940492390.0006690181981945830.00545530852601843
TCF7L2#6934310.77017656313730.0008003181298398380.00617132495291959
TFAP2A#7020316.5186343730450.0002218033880766340.00249380170603247
TRIM28#10155318.59052504526250.0001555969297255280.00198030559878191
USF1#739136.361499277207960.00388404057290560.0191080744921423
YY1#752834.911170749853860.008441455341808260.033108650835328
ZBTB7A#5134137.35190930787590.002516255860282270.0140871211896017
ZNF263#1012738.221841637010680.001799043925565870.0110076951515715



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.