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Coexpression cluster:C1455: Difference between revisions

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|tf_chipseq_enrich=HEY1#23462;5:3.36675920258809:0.00442382704520303:0.0209523410627164!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380336971519365!STAT3#6774;3:5.25973249857712:0.0137766205807855:0.0484743776307749!TAF1#6872;5:2.78587190478774:0.0107863634029041:0.0397950052082767!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0296076080502154!USF2#7392;4:8.66146492337973:0.000463535508143562:0.0042679348439571
|tf_chipseq_enrich=HEY1#23462;5:3.36675920258809:0.00442382704520303:0.0209523410627164!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380336971519365!STAT3#6774;3:5.25973249857712:0.0137766205807855:0.0484743776307749!TAF1#6872;5:2.78587190478774:0.0107863634029041:0.0397950052082767!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0296076080502154!USF2#7392;4:8.66146492337973:0.000463535508143562:0.0042679348439571
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}}
}}

Revision as of 14:54, 26 November 2012


Full id: C1455_Tracheal_Corneal_Keratinocyte_Mammary_Urothelial_Bronchial_Esophageal



Phase1 CAGE Peaks

Hg19::chr19:45281118..45281181,+p1@CBLC
Hg19::chr19:45281215..45281224,+p2@CU688574
Hg19::chr19:45281245..45281260,+p1@CU688574
Hg19::chr1:26856236..26856292,+p2@RPS6KA1
Hg19::chr22:37915562..37915598,-p3@CARD10
Hg19::chr22:40390930..40390994,+p1@FAM83F


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


GO IDGO nameFDR corrected p-value
GO:0007175negative regulation of epidermal growth factor receptor activity0.00847707066194942
GO:0042059negative regulation of epidermal growth factor receptor signaling pathway0.00847707066194942
GO:0032449CBM complex0.00847707066194942
GO:0007176regulation of epidermal growth factor receptor activity0.0158169451647997
GO:0007250activation of NF-kappaB-inducing kinase0.0158169451647997
GO:0042058regulation of epidermal growth factor receptor signaling pathway0.0158169451647997
GO:0065009regulation of a molecular function0.0158169451647997
GO:0030159receptor signaling complex scaffold activity0.0188285090913903
GO:0032947protein complex scaffold0.0188285090913903
GO:0007173epidermal growth factor receptor signaling pathway0.0277273132276541
GO:0006468protein amino acid phosphorylation0.0277273132276541
GO:0007165signal transduction0.0277273132276541
GO:0007154cell communication0.0323588363159623
GO:0016310phosphorylation0.032800513276824
GO:0019538protein metabolic process0.032800513276824
GO:0032147activation of protein kinase activity0.0370140841269794
GO:0006793phosphorus metabolic process0.0385749904955098
GO:0006796phosphate metabolic process0.0385749904955098
GO:0009968negative regulation of signal transduction0.0462629851426927



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>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.04e-25160
endoderm3.04e-25160
presumptive endoderm3.04e-25160
digestive system9.41e-20145
digestive tract9.41e-20145
primitive gut9.41e-20145
subdivision of digestive tract1.34e-17118
renal system5.17e-1548
urinary system structure1.18e-1447
immaterial anatomical entity7.09e-14117
trunk region element5.82e-13101
endo-epithelium6.87e-1382
organ1.47e-12503
anatomical space4.47e-1295
organism subdivision6.05e-12264
embryo4.22e-11592
respiratory system4.17e-1074
foregut4.33e-1087
organ part4.66e-10218
orifice5.53e-1036
multi-cellular organism9.43e-10656
multi-tissue structure2.08e-09342
developing anatomical structure2.85e-09581
subdivision of trunk3.12e-09112
anatomical system1.65e-08624
kidney1.66e-0826
kidney mesenchyme1.66e-0826
upper urinary tract1.66e-0826
kidney rudiment1.66e-0826
kidney field1.66e-0826
anterior region of body1.70e-0862
craniocervical region1.70e-0862
nephron tubule epithelium1.80e-0810
anatomical group2.06e-08625
excretory tube2.20e-0816
kidney epithelium2.20e-0816
reproductive structure2.56e-0859
reproductive system2.56e-0859
epithelial bud3.27e-0837
nephron epithelium4.00e-0815
renal tubule4.00e-0815
nephron tubule4.00e-0815
nephron4.00e-0815
uriniferous tubule4.00e-0815
nephrogenic mesenchyme4.00e-0815
head4.15e-0856
exocrine gland5.07e-0831
exocrine system5.07e-0831
primordium5.73e-08160
abdomen element6.61e-0854
abdominal segment element6.61e-0854
oral opening7.60e-0822
cavitated compound organ8.24e-0831
gland2.59e-0759
gut epithelium3.96e-0754
subdivision of head4.04e-0749
reproductive organ5.27e-0748
intestine6.93e-0717
gastrointestinal system7.05e-0725
anatomical cavity8.35e-0761
Disease
Ontology termp-valuen
carcinoma3.50e-14106
squamous cell carcinoma5.95e-1014
cell type cancer1.76e-08143


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
HEY1#2346253.366759202588090.004423827045203030.0209523410627164
POLR2A#543062.147453176558070.01019570676818780.0380336971519365
STAT3#677435.259732498577120.01377662058078550.0484743776307749
TAF1#687252.785871904787740.01078636340290410.0397950052082767
USF1#739144.240999518138640.007005367750829420.0296076080502154
USF2#739248.661464923379730.0004635355081435620.0042679348439571



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.