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Coexpression cluster:C4847: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281813380096311!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066975075633891!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00204204777921587!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331609551810394
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281813380096311!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066975075633891!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00204204777921587!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331609551810394
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}}
}}

Revision as of 17:00, 26 November 2012


Full id: C4847_neuroblastoma_gastrointestinal_cervical_Chondrocyte_uterus_Renal_kidney



Phase1 CAGE Peaks

Hg19::chrX:117250709..117250720,-p3@KLHL13
Hg19::chrX:117250723..117250739,-p2@KLHL13
Hg19::chrX:117250740..117250792,-p1@KLHL13


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
anatomical cluster1.07e-23373
multi-tissue structure1.53e-17342
organ system subdivision1.05e-11223
multi-cellular organism1.84e-11656
anatomical conduit5.86e-11240
adult organism9.45e-11114
organ part7.27e-10218
compound organ7.76e-1068
embryo1.07e-09592
structure with developmental contribution from neural crest1.83e-09132
anatomical system2.17e-09624
ectoderm-derived structure2.80e-09171
ectoderm2.80e-09171
presumptive ectoderm2.80e-09171
epithelium3.35e-09306
anatomical group3.57e-09625
cell layer4.15e-09309
developing anatomical structure7.33e-09581
digestive system1.48e-08145
digestive tract1.48e-08145
primitive gut1.48e-08145
orifice2.02e-0836
neurectoderm2.39e-0886
neural plate4.11e-0882
presumptive neural plate4.11e-0882
organ1.06e-07503
subdivision of head1.45e-0749
mouth1.55e-0729
stomodeum1.55e-0729
larynx2.14e-079
head3.52e-0756
anterior region of body3.95e-0762
craniocervical region3.95e-0762
ecto-epithelium5.11e-07104
endoderm-derived structure7.55e-07160
endoderm7.55e-07160
presumptive endoderm7.55e-07160


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
CTCF#1066435.360256373075030.0064925092527670.0281813380096311
RAD21#5885310.35503389545630.0009004912073565420.0066975075633891
SMARCB1#6598318.25271578115740.000164397760679890.00204204777921587
YY1#752834.911170749853860.008441455341808260.0331609551810394



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.