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Coexpression cluster:C3674: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3674_Small_Urothelial_Prostate_Esophageal_Alveolar_chorionic_Mammary
|full_id=C3674_Small_Urothelial_Prostate_Esophageal_Alveolar_chorionic_Mammary
|id=C3674
|id=C3674

Revision as of 16:38, 12 September 2012


Full id: C3674_Small_Urothelial_Prostate_Esophageal_Alveolar_chorionic_Mammary



Phase1 CAGE Peaks

Hg19::chr17:7255461..7255518,+p1@KCTD11
Hg19::chr17:7255547..7255558,+p3@KCTD11
Hg19::chr17:7255566..7255590,+p2@KCTD11


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
multi-cellular organism1.01e-14659
organism subdivision2.94e-14365
trunk1.39e-12216
anatomical system1.70e-12625
anatomical group2.63e-12626
mesenchyme9.14e-11238
entire embryonic mesenchyme9.14e-11238
surface structure1.51e-0995
multilaminar epithelium3.52e-0982
multi-tissue structure1.27e-08347
embryonic structure5.82e-08605
developing anatomical structure5.82e-08605
germ layer1.05e-07604
embryonic tissue1.05e-07604
presumptive structure1.05e-07604
epiblast (generic)1.05e-07604
embryo1.14e-07612
subdivision of trunk1.57e-07113
somite1.84e-0783
paraxial mesoderm1.84e-0783
presomitic mesoderm1.84e-0783
presumptive segmental plate1.84e-0783
trunk paraxial mesoderm1.84e-0783
presumptive paraxial mesoderm1.84e-0783
trunk mesenchyme1.95e-07143
mesoderm3.11e-07448
mesoderm-derived structure3.11e-07448
presumptive mesoderm3.11e-07448
skeletal muscle tissue3.55e-0761
striated muscle tissue3.55e-0761
myotome3.55e-0761
thoracic segment of trunk4.81e-0752
organ5.24e-07511
compound organ5.73e-0769
tracheobronchial tree6.09e-0714
lower respiratory tract6.09e-0714
muscle tissue7.82e-0763
musculature7.82e-0763
musculature of body7.82e-0763


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
CHD2#1106310.34402283411690.0009033701102746880.00660000496306248
EGR1#195834.988179094810140.008056488137383440.032033028689237
ELF1#199734.258097958807540.01295179875054610.0461789194902459
ESR1#2099330.76860329615453.43136389821584e-050.000675656512378891
ETS1#211339.728760922202340.001085840092584840.00761663331516339
FOS#235338.99795530889440.001372499272417130.00896787109058887
FOSL2#2355316.93020060456170.0002060162053171620.00242845671186445
MYC#460935.22228187160940.007020843755740150.0294229726337525
NFKB1#479035.488063424193840.006049381815655430.0269397657958911
PAX5#507936.669565531177830.003370290999677260.0172798145171965
TCF7L2#6934310.77017656313730.0008003181298398380.00613103683432428
TFAP2A#7020316.5186343730450.0002218033880766340.00248018458750916
TFAP2C#7022310.80922860986020.0007916746575753130.00615145521631635



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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