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Coexpression cluster:C3613: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189811172084913!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324838013704494!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321644742546973!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320184011788953!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461631598426143!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.012791698905166!JUND#3727;3:6.99466394187103:0.00292184504273499:0.01565457212426!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195011530266025!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294147104061997!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269317271599488!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172755740719163!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00881418027779025!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.0020290165123667!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246165857113498!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542144565496928!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00628806584597852!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242571372156194!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388709497554471
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189811172084913!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324838013704494!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321644742546973!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320184011788953!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461631598426143!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.012791698905166!JUND#3727;3:6.99466394187103:0.00292184504273499:0.01565457212426!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195011530266025!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294147104061997!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269317271599488!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172755740719163!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00881418027779025!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.0020290165123667!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246165857113498!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542144565496928!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00628806584597852!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242571372156194!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388709497554471
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}}
}}

Revision as of 16:14, 26 November 2012


Full id: C3613_optic_Hep2_corpus_lens_Mesenchymal_globus_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr17:20059323..20059342,+p4@SPECC1
Hg19::chr17:20059346..20059355,+p5@SPECC1
Hg19::chr17:20059358..20059401,+p1@SPECC1


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 cell2.51e-17253
endo-epithelial cell1.55e-0742
Uber Anatomy
Ontology termp-valuen
central nervous system6.94e-1981
nervous system8.35e-1789
organ system subdivision1.35e-15223
neural tube3.05e-1556
neural rod3.05e-1556
future spinal cord3.05e-1556
neural keel3.05e-1556
brain3.42e-1568
future brain3.42e-1568
regional part of nervous system7.55e-1453
regional part of brain7.55e-1453
organ part8.55e-13218
ecto-epithelium2.61e-12104
ectoderm-derived structure4.52e-12171
ectoderm4.52e-12171
presumptive ectoderm4.52e-12171
neural plate4.88e-1282
presumptive neural plate4.88e-1282
brain grey matter2.69e-1134
gray matter2.69e-1134
telencephalon3.32e-1134
regional part of forebrain7.15e-1141
forebrain7.15e-1141
anterior neural tube7.15e-1141
future forebrain7.15e-1141
pre-chordal neural plate2.46e-1061
regional part of telencephalon2.76e-1032
neurectoderm3.14e-1086
cerebral hemisphere4.04e-1032
larynx1.37e-079
cerebral cortex1.45e-0725
pallium1.45e-0725
multi-tissue structure3.92e-07342
regional part of cerebral cortex6.94e-0722
structure with developmental contribution from neural crest7.22e-07132
Disease
Ontology termp-valuen
carcinoma2.42e-12106
cell type cancer2.98e-09143
reproductive organ cancer2.65e-0729
disease of cellular proliferation2.78e-07239
cancer2.84e-07235


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#90536.336201576962630.003930750035764890.0189811172084913
E2F1#186934.907389214879320.008460985347239390.0324838013704494
E2F6#187635.017155731697390.00791769806886330.0321644742546973
EGR1#195834.988179094810140.008056488137383440.0320184011788953
ELF1#199734.258097958807540.01295179875054610.0461631598426143
IRF1#365937.63716375356390.002244692747297240.012791698905166
JUND#372736.994663941871030.002921845042734990.01565457212426
MEF2A#4205318.74323090964410.0001518243905622470.00195011530266025
MYC#460935.22228187160940.007020843755740150.0294147104061997
NFKB1#479035.488063424193840.006049381815655430.0269317271599488
PAX5#507936.669565531177830.003370290999677260.0172755740719163
POU2F2#545239.106124057742520.001324165192682130.00881418027779025
SMARCB1#6598318.25271578115740.000164397760679890.0020290165123667
SP1#666735.69838137814090.005403962701712170.0246165857113498
TAF7#6879311.43306940492390.0006690181981945830.00542144565496928
TCF12#6938310.63446490218640.0008313523990202070.00628806584597852
ZEB1#6935316.88843201754390.0002075486917327580.00242571372156194
ZNF143#7702313.50087655222790.0004062804962997170.00388709497554471



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.