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Coexpression cluster:C4718: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191216918806302!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281380684641768!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327826692146294!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324433642739334!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322590025909669!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168523165404464!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000679371022115192!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.010925489450131!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187439945480208!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.0072354090314076!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296142932554825!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00473616541483056!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173710616253908!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00668845752116562!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278340814010737!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310905162318209!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376547704754258!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617542853064964!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249487604171627!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618921398027608!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191233883364929!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423306586833399!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331322918727916!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243826522113358
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191216918806302!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281380684641768!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327826692146294!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324433642739334!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322590025909669!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168523165404464!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000679371022115192!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.010925489450131!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187439945480208!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.0072354090314076!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296142932554825!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00473616541483056!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173710616253908!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00668845752116562!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278340814010737!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310905162318209!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376547704754258!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617542853064964!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249487604171627!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618921398027608!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191233883364929!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423306586833399!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331322918727916!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243826522113358
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}}
}}

Revision as of 16:55, 26 November 2012


Full id: C4718_cerebellum_pancreas_occipital_pharyngeal_Hepatocyte_cervical_rectal



Phase1 CAGE Peaks

Hg19::chr8:110656917..110656960,-p4@SYBU
Hg19::chr8:110656962..110656982,-p3@SYBU
Hg19::chr8:110656995..110657075,-p1@SYBU


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell2.30e-08253
endodermal cell4.73e-0858
Uber Anatomy
Ontology termp-valuen
adult organism1.89e-33114
organ system subdivision1.13e-31223
neural tube1.12e-2356
neural rod1.12e-2356
future spinal cord1.12e-2356
neural keel1.12e-2356
regional part of nervous system3.06e-2253
regional part of brain3.06e-2253
anatomical cluster1.33e-21373
central nervous system2.92e-2081
brain8.92e-2068
future brain8.92e-2068
neural plate1.09e-1982
presumptive neural plate1.09e-1982
ecto-epithelium1.37e-19104
neurectoderm7.28e-1886
regional part of forebrain1.37e-1741
forebrain1.37e-1741
anterior neural tube1.37e-1741
future forebrain1.37e-1741
nervous system2.79e-1789
multi-tissue structure5.27e-17342
ectoderm-derived structure8.98e-17171
ectoderm8.98e-17171
presumptive ectoderm8.98e-17171
organ part4.92e-16218
brain grey matter1.32e-1534
gray matter1.32e-1534
telencephalon3.06e-1534
cerebral hemisphere8.74e-1532
regional part of telencephalon1.49e-1432
regional part of cerebral cortex2.50e-1422
pre-chordal neural plate6.30e-1461
neocortex2.72e-1320
digestive system3.10e-13145
digestive tract3.10e-13145
primitive gut3.10e-13145
anatomical conduit3.33e-12240
organ5.20e-12503
endoderm-derived structure5.84e-12160
endoderm5.84e-12160
presumptive endoderm5.84e-12160
cerebral cortex1.17e-1125
pallium1.17e-1125
subdivision of digestive tract1.48e-11118
structure with developmental contribution from neural crest1.60e-11132
respiratory system3.24e-0974
organ segment1.93e-0898
foregut3.39e-0887
respiratory primordium3.51e-0838
endoderm of foregut3.51e-0838
tube3.77e-08192
posterior neural tube2.66e-0715
chordal neural plate2.66e-0715
respiratory tract7.31e-0754
Disease
Ontology termp-valuen
carcinoma2.01e-10106
cell type cancer3.16e-07143


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#90536.336201576962630.003930750035764890.0191216918806302
CTCF#1066435.360256373075030.0064925092527670.0281380684641768
E2F1#186934.907389214879320.008460985347239390.0327826692146294
E2F6#187635.017155731697390.00791769806886330.0324433642739334
EGR1#195834.988179094810140.008056488137383440.0322590025909669
EP300#203336.77394172622320.003216880500103790.0168523165404464
ESR1#2099330.76860329615453.43136389821584e-050.000679371022115192
HMGN3#932438.178547723350590.001827766942164210.010925489450131
MAX#414936.452555509007120.003721913834265510.0187439945480208
MXI1#460139.96157162875930.001011470541259020.0072354090314076
MYC#460935.22228187160940.007020843755740150.0296142932554825
NRF1#4899312.21027944771090.0005492172401020010.00473616541483056
PAX5#507936.669565531177830.003370290999677260.0173710616253908
RAD21#5885310.35503389545630.0009004912073565420.00668845752116562
SIN3A#2594235.408884726815140.006318961977991520.0278340814010737
SMC3#9126315.04493284493280.0002935825420371870.00310905162318209
SRF#6722313.79717826216780.0003806615025800190.00376547704754258
TCF7L2#6934310.77017656313730.0008003181298398380.00617542853064964
TFAP2A#7020316.5186343730450.0002218033880766340.00249487604171627
TFAP2C#7022310.80922860986020.0007916746575753130.00618921398027608
USF1#739136.361499277207960.00388404057290560.0191233883364929
USF2#7392312.99219738506960.0004558979393427810.00423306586833399
YY1#752834.911170749853860.008441455341808260.0331322918727916
ZEB1#6935316.88843201754390.0002075486917327580.00243826522113358



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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