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Coexpression cluster:C4279: Difference between revisions

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|tf_chipseq_enrich=BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273925321245613!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190577783290121!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438026304750861!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032335528432879!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463720572405994!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.000628796204628547!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108943129592905!JUNB#3726;2:20.4070884398808:0.00313146219943874:0.0164518728631814!SETDB1#9869;2:26.880017452007:0.00181446890796441:0.010896516490075!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390287871630684!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330366916901414
|tf_chipseq_enrich=BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273925321245613!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190577783290121!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438026304750861!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032335528432879!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463720572405994!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.000628796204628547!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108943129592905!JUNB#3726;2:20.4070884398808:0.00313146219943874:0.0164518728631814!SETDB1#9869;2:26.880017452007:0.00181446890796441:0.010896516490075!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390287871630684!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330366916901414
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}}
}}

Revision as of 16:39, 26 November 2012


Full id: C4279_skeletal_diaphragm_heart_tongue_left_penis_throat



Phase1 CAGE Peaks

Hg19::chr3:12838161..12838215,+p1@CAND2
Hg19::chr6:146056648..146056679,-p2@EPM2A
Hg19::chr6:146056691..146056735,-p3@EPM2A


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

GO IDGO nameFDR corrected p-value
GO:0017025TATA-binding protein binding0.00777099123786688
GO:0005844polysome0.0174829288234617
GO:0005977glycogen metabolic process0.0370821653336492
GO:0006073glucan metabolic process0.0370821653336492
GO:0006112energy reserve metabolic process0.0370821653336492
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.0370821653336492
GO:0043687post-translational protein modification0.0370821653336492
GO:0044264cellular polysaccharide metabolic process0.0370821653336492
GO:0005976polysaccharide metabolic process0.0370821653336492
GO:0006464protein modification process0.0378194588250887
GO:0043412biopolymer modification0.0378194588250887
GO:0015980energy derivation by oxidation of organic compounds0.0378194588250887



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.53e-42114
nervous system4.68e-3089
central nervous system2.75e-2981
neural tube1.11e-2656
neural rod1.11e-2656
future spinal cord1.11e-2656
neural keel1.11e-2656
brain5.31e-2568
future brain5.31e-2568
regional part of nervous system6.73e-2553
regional part of brain6.73e-2553
regional part of forebrain3.41e-2241
forebrain3.41e-2241
anterior neural tube3.41e-2241
future forebrain3.41e-2241
ectoderm-derived structure5.37e-21171
ectoderm5.37e-21171
presumptive ectoderm5.37e-21171
neurectoderm5.48e-2086
neural plate1.10e-1982
presumptive neural plate1.10e-1982
brain grey matter1.24e-1834
gray matter1.24e-1834
telencephalon1.37e-1834
cerebral hemisphere2.05e-1732
regional part of telencephalon2.11e-1732
organ system subdivision1.06e-16223
pre-chordal neural plate1.01e-1561
ecto-epithelium4.32e-15104
structure with developmental contribution from neural crest6.40e-14132
cerebral cortex1.77e-1325
pallium1.77e-1325
regional part of cerebral cortex9.12e-1322
neocortex9.62e-1220
organ1.09e-08503
multi-cellular organism1.64e-08656
anatomical cluster2.97e-08373
germ layer3.93e-07560
germ layer / neural crest3.93e-07560
embryonic tissue3.93e-07560
presumptive structure3.93e-07560
germ layer / neural crest derived structure3.93e-07560
epiblast (generic)3.93e-07560
anatomical group8.88e-07625


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
BCLAF1#9774214.43509840674790.006201147435546130.0273925321245613
CCNT2#90536.336201576962630.003930750035764890.0190577783290121
E2F4#1874312.66806031528440.0004917987006298980.00438026304750861
E2F6#187635.017155731697390.00791769806886330.032335528432879
ELF1#199734.258097958807540.01295179875054610.0463720572405994
GTF2B#2959331.94382993432423.06634405746243e-050.000628796204628547
HMGN3#932438.178547723350590.001827766942164210.0108943129592905
JUNB#3726220.40708843988080.003131462199438740.0164518728631814
SETDB1#9869226.8800174520070.001814468907964410.010896516490075
TFAP2A#7020211.01242291536330.01054990655215560.0390287871630684
YY1#752834.911170749853860.008441455341808260.0330366916901414



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.

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