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Coexpression cluster:C4476: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019084356979464!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280844588241275!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172213200263853!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327110701369784!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032386185274508!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322046757982236!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464389216461234!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154671342435563!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667279702037107!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0330093837962358!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249192384330202!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618088581614025!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330838019529838!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140742955115692
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019084356979464!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280844588241275!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172213200263853!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327110701369784!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032386185274508!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322046757982236!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464389216461234!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154671342435563!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667279702037107!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0330093837962358!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249192384330202!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618088581614025!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330838019529838!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140742955115692
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}}
}}

Revision as of 16:45, 26 November 2012


Full id: C4476_Chondrocyte_Preadipocyte_Adipocyte_myxofibrosarcoma_Osteoblast_Fibroblast_occipital



Phase1 CAGE Peaks

Hg19::chr5:14871734..14871751,-p3@ANKH
Hg19::chr5:14871759..14871775,-p7@ANKH
Hg19::chr5:14871789..14871813,-p6@ANKH


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>

Cell Type
Ontology termp-valuen
preadipocyte1.59e-0712
Uber Anatomy
Ontology termp-valuen
adult organism8.41e-21114
neural tube4.78e-1956
neural rod4.78e-1956
future spinal cord4.78e-1956
neural keel4.78e-1956
brain3.33e-1868
future brain3.33e-1868
regional part of nervous system3.82e-1853
regional part of brain3.82e-1853
central nervous system1.44e-1681
neural plate3.72e-1682
presumptive neural plate3.72e-1682
regional part of forebrain5.64e-1641
forebrain5.64e-1641
anterior neural tube5.64e-1641
future forebrain5.64e-1641
nervous system1.02e-1589
neurectoderm1.04e-1486
telencephalon7.61e-1434
brain grey matter1.52e-1334
gray matter1.52e-1334
ecto-epithelium1.88e-13104
cerebral hemisphere6.97e-1332
regional part of telencephalon9.78e-1332
regional part of cerebral cortex2.28e-1222
ectoderm-derived structure2.34e-12171
ectoderm2.34e-12171
presumptive ectoderm2.34e-12171
structure with developmental contribution from neural crest4.17e-12132
pre-chordal neural plate8.71e-1261
organ system subdivision1.50e-11223
neocortex1.77e-1120
cerebral cortex4.66e-1025
pallium4.66e-1025
multi-cellular organism9.22e-10656
anatomical system1.36e-08624
organ1.78e-08503
anatomical group2.00e-08625
germ layer4.96e-08560
germ layer / neural crest4.96e-08560
embryonic tissue4.96e-08560
presumptive structure4.96e-08560
germ layer / neural crest derived structure4.96e-08560
epiblast (generic)4.96e-08560
multi-tissue structure7.78e-08342
embryonic structure1.35e-07564


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#90536.336201576962630.003930750035764890.019084356979464
CTCF#1066435.360256373075030.0064925092527670.0280844588241275
CTCFL#140690319.74647435897440.0001298372005551160.00172213200263853
E2F1#186934.907389214879320.008460985347239390.0327110701369784
E2F6#187635.017155731697390.00791769806886330.032386185274508
EGR1#195834.988179094810140.008056488137383440.0322046757982236
ELF1#199734.258097958807540.01295179875054610.0464389216461234
GABPB1#255337.067683836182170.002832212825417420.0154671342435563
RAD21#5885310.35503389545630.0009004912073565420.00667279702037107
SMARCB1#6598212.16847718743830.008675002221921740.0330093837962358
TFAP2A#7020316.5186343730450.0002218033880766340.00249192384330202
TFAP2C#7022310.80922860986020.0007916746575753130.00618088581614025
YY1#752834.911170749853860.008441455341808260.0330838019529838
ZBTB7A#5134137.35190930787590.002516255860282270.0140742955115692



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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