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Coexpression cluster:C4113: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00110022846608685!BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000778364143358186!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00916680117329771!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00898980567651129!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270054023272168!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173206289595165!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136886791614487!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630175738142483
|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00110022846608685!BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000778364143358186!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00916680117329771!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00898980567651129!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270054023272168!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173206289595165!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136886791614487!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630175738142483
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}}
}}

Revision as of 16:33, 26 November 2012


Full id: C4113_Sertoli_Fibroblast_Cardiac_Mesenchymal_Hair_Smooth_liver



Phase1 CAGE Peaks

Hg19::chr2:102720988..102721019,+p8@IL1R1
Hg19::chr2:102721025..102721051,+p3@IL1R1
Hg19::chr2:102721057..102721110,+p2@IL1R1


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
somite2.46e-1671
presomitic mesoderm2.46e-1671
presumptive segmental plate2.46e-1671
dermomyotome2.46e-1671
trunk paraxial mesoderm2.46e-1671
paraxial mesoderm3.48e-1672
presumptive paraxial mesoderm3.48e-1672
dense mesenchyme tissue1.53e-1573
muscle tissue5.21e-1464
musculature5.21e-1464
musculature of body5.21e-1464
skeletal muscle tissue9.91e-1462
striated muscle tissue9.91e-1462
myotome9.91e-1462
trunk mesenchyme2.78e-13122
multi-cellular organism3.78e-13656
tissue3.94e-13773
multi-tissue structure6.84e-13342
epithelial vesicle1.32e-1278
mesoderm1.95e-12315
mesoderm-derived structure1.95e-12315
presumptive mesoderm1.95e-12315
anatomical system2.00e-12624
anatomical group3.33e-12625
multilaminar epithelium3.55e-1283
musculoskeletal system3.90e-11167
primary circulatory organ4.41e-1127
mesenchyme4.43e-11160
entire embryonic mesenchyme4.43e-11160
heart5.42e-1124
primitive heart tube5.42e-1124
primary heart field5.42e-1124
anterior lateral plate mesoderm5.42e-1124
heart tube5.42e-1124
heart primordium5.42e-1124
cardiac mesoderm5.42e-1124
cardiogenic plate5.42e-1124
heart rudiment5.42e-1124
splanchnic layer of lateral plate mesoderm8.36e-1183
embryonic structure8.54e-11564
germ layer1.52e-10560
germ layer / neural crest1.52e-10560
embryonic tissue1.52e-10560
presumptive structure1.52e-10560
germ layer / neural crest derived structure1.52e-10560
epiblast (generic)1.52e-10560
organ3.17e-09503
developing anatomical structure4.35e-09581
unilaminar epithelium7.57e-09148
organism subdivision8.73e-08264
embryo9.21e-08592
anatomical cluster4.86e-07373
trunk6.05e-07199
epithelial tube9.75e-07117


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
BATF#10538324.35780179230366.91705216281876e-050.00110022846608685
BCL11A#53335328.36945510360714.37778126761649e-050.000778364143358186
EBF1#187938.9064668465690.00141523283560980.00916680117329771
FOS#235338.99795530889440.001372499272417130.00898980567651129
NFKB1#479035.488063424193840.006049381815655430.0270054023272168
PAX5#507936.669565531177830.003370290999677260.0173206289595165
PBX3#5090321.91451268674419.49854535978121e-050.00136886791614487
TCF12#6938310.63446490218640.0008313523990202070.00630175738142483



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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