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Coexpression cluster:C2843

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Full id: C2843_CD4_cholangiocellular_seminal_ductus_Mesenchymal_caudate_Fibroblast



Phase1 CAGE Peaks

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 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
adult organism2.88e-17115
musculoskeletal system3.98e-14167
regional part of brain9.30e-1459
neural tube9.71e-1357
neural rod9.71e-1357
future spinal cord9.71e-1357
neural keel9.71e-1357
neural plate4.79e-1286
presumptive neural plate4.79e-1286
neurectoderm5.64e-1290
regional part of forebrain5.73e-1241
forebrain5.73e-1241
future forebrain5.73e-1241
anterior neural tube7.03e-1242
somite8.32e-1283
paraxial mesoderm8.32e-1283
presomitic mesoderm8.32e-1283
presumptive segmental plate8.32e-1283
trunk paraxial mesoderm8.32e-1283
presumptive paraxial mesoderm8.32e-1283
brain1.02e-1169
future brain1.02e-1169
pre-chordal neural plate1.72e-1161
anterior region of body2.37e-11129
craniocervical region2.37e-11129
gray matter8.41e-1134
brain grey matter8.41e-1134
cerebral hemisphere1.15e-1032
telencephalon1.52e-1034
head2.20e-10123
dermomyotome3.07e-1070
muscle tissue3.52e-1063
musculature3.52e-1063
musculature of body3.52e-1063
regional part of telencephalon4.60e-1033
central nervous system6.00e-1082
skeletal muscle tissue1.17e-0961
striated muscle tissue1.17e-0961
myotome1.17e-0961
regional part of cerebral cortex7.25e-0922
neocortex1.26e-0820
multi-tissue structure7.53e-08347
regional part of nervous system1.28e-0794
nervous system1.28e-0794
cerebral cortex3.13e-0725
pallium3.13e-0725
anatomical cluster7.10e-07286


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
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 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.