Personal tools

Coexpression cluster:C2843

From FANTOM5_SSTAR

Revision as of 05:29, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2843_CD4_cholangiocellular_seminal_ductus_Mesenchymal_caudate_Fibroblast



Phase1 CAGE Peaks

  Short description
Hg19::chr6:136172724..136172738,+ p6@PDE7B
Hg19::chr6:136172786..136172816,+ p4@PDE7B
Hg19::chr6:136172820..136172846,+ p2@PDE7B
Hg19::chr6:136173008..136173013,+ p1@PDE7B


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


Uber Anatomy
Ontology termp-valuen
adult organism2.61e-16114
musculoskeletal system1.98e-14167
structure with developmental contribution from neural crest3.35e-14132
neural plate2.31e-1282
presumptive neural plate2.31e-1282
neurectoderm2.88e-1286
neural tube5.25e-1256
neural rod5.25e-1256
future spinal cord5.25e-1256
neural keel5.25e-1256
regional part of forebrain9.48e-1241
forebrain9.48e-1241
anterior neural tube9.48e-1241
future forebrain9.48e-1241
regional part of nervous system5.83e-1153
regional part of brain5.83e-1153
pre-chordal neural plate6.06e-1161
brain grey matter1.01e-1034
gray matter1.01e-1034
brain1.12e-1068
future brain1.12e-1068
cerebral hemisphere1.33e-1032
dense mesenchyme tissue1.78e-1073
telencephalon1.85e-1034
regional part of telencephalon4.25e-1032
paraxial mesoderm4.44e-1072
presumptive paraxial mesoderm4.44e-1072
somite6.37e-1071
presomitic mesoderm6.37e-1071
presumptive segmental plate6.37e-1071
dermomyotome6.37e-1071
trunk paraxial mesoderm6.37e-1071
muscle tissue9.08e-1064
musculature9.08e-1064
musculature of body9.08e-1064
skeletal muscle tissue2.65e-0962
striated muscle tissue2.65e-0962
myotome2.65e-0962
central nervous system4.68e-0981
multi-tissue structure6.67e-09342
regional part of cerebral cortex7.99e-0922
neocortex1.14e-0820
ecto-epithelium1.62e-07104
cerebral cortex3.53e-0725
pallium3.53e-0725
epithelial vesicle3.72e-0778
nervous system3.92e-0789


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
BRCA1#672420.18423064322386.02116732184487e-060.000179772639773058
CEBPB#105147.971147625824820.0002476385788090830.00268568281747059
EP300#203346.77394172622320.0004748459821442640.0043513590882833
JUND#372746.994663941871030.000417684217818580.00392430029010028
MAX#414946.452555509007120.0005767613195645490.00486326299483303
MYC#460945.22228187160940.001344309395272740.00889610498877768
RAD21#5885410.35503389545638.6948481184721e-050.00129837180818574
REST#597849.650028716128020.0001152825614219170.0015746789736259
RFX5#5993412.04791082719514.74457429336527e-050.000828349372492102
SMC3#9126415.04493284493281.95092670935632e-050.000439501368849147
TAF1#687243.343046285745290.008005664898701650.0323219281102328
TBP#690843.706770687096390.005296377814784350.0244951024089214
TFAP2A#7020416.5186343730451.34240829060362e-050.000327263724235181
TFAP2C#7022410.80922860986027.32289634782688e-050.00114816990192267
TRIM28#10155418.59052504526258.36730015875654e-060.000230816814918218



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.