Personal tools

Coexpression cluster:C3887

From FANTOM5_SSTAR

Revision as of 07:24, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3887_Mesenchymal_Preadipocyte_Hepatocyte_Endothelial_bone_Adipocyte_kidney



Phase1 CAGE Peaks

  Short description
Hg19::chr1:159750776..159750808,+ p2@DUSP23
Hg19::chr1:159750811..159750831,+ p4@DUSP23
Hg19::chr1:159750957..159750987,+ p3@DUSP23


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
epithelial cell2.84e-11253
endothelial cell3.01e-0936
lining cell1.31e-0858
barrier cell1.31e-0858
meso-epithelial cell2.43e-0745
Uber Anatomy
Ontology termp-valuen
primordium1.13e-08160
subdivision of trunk6.48e-08112
immaterial anatomical entity7.20e-07117


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0190118836190084
CHD2#1106310.34402283411690.0009033701102746880.00660601252954615
E2F1#186934.907389214879320.008460985347239390.0325496113408109
E2F6#187635.017155731697390.00791769806886330.0322384588153612
EGR1#195834.988179094810140.008056488137383440.0320794374387201
ELF1#199734.258097958807540.01295179875054610.0462499712691313
ETS1#211339.728760922202340.001085840092584840.00762739127182323
FOS#235338.99795530889440.001372499272417130.00897910620846734
GATA3#2625218.15767757147070.003944546819279620.0189513536322911
MAX#414936.452555509007120.003721913834265510.0186621037465483
MYC#460935.22228187160940.007020843755740150.0294655375127887
NANOG#79923219.49651898734180.003427255648501020.0174476798768607
NFYA#4800318.42558069983050.0001598135507814160.00199769807660806
NFYB#4801316.75979325353650.0002123649923296180.00245943528874617
PBX3#5090321.91451268674419.49854535978121e-050.00136679330232873
SIN3A#2594235.408884726815140.006318961977991520.0276915940760094
SMC3#9126210.02995522995520.0126656379767470.0457505815603182
SP1#666735.69838137814090.005403962701712170.0246639190929562
TAF7#6879311.43306940492390.0006690181981945830.00543240488269663
USF1#739136.361499277207960.00388404057290560.0190372307768767
USF2#7392312.99219738506960.0004558979393427810.00421806563492388
ZBTB7A#5134137.35190930787590.002516255860282270.0140277167605434
ZEB1#6935316.88843201754390.0002075486917327580.00242870339673697



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.