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Coexpression cluster:C2811: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268484641671772!ELK4#2005;4:16.235681658468:1.43847748454449e-05:0.000343625686203893!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195297819772855!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000723898078634292!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387136570250642!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123370970542737!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244864277378602
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268484641671772!ELK4#2005;4:16.235681658468:1.43847748454449e-05:0.000343625686203893!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195297819772855!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000723898078634292!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387136570250642!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123370970542737!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244864277378602
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}}
}}

Revision as of 15:44, 26 November 2012


Full id: C2811_cervical_epitheloid_ductal_tongue_esophagus_immature_salivary



Phase1 CAGE Peaks

Hg19::chr5:147470499..147470536,+p4@SPINK5
Hg19::chr5:147470546..147470574,+p3@SPINK5
Hg19::chr5:147470578..147470587,+p9@SPINK5
Hg19::chr5:147470611..147470637,+p@chr5:147470611..147470637
+


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>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.73e-15160
endoderm9.73e-15160
presumptive endoderm9.73e-15160
respiratory system2.45e-1474
oral opening7.94e-1222
digestive system3.19e-11145
digestive tract3.19e-11145
primitive gut3.19e-11145
orifice1.65e-1036
mucosa2.77e-1020
mouth3.76e-1029
stomodeum3.76e-1029
respiratory tract4.19e-0954
anterior region of body1.69e-0862
craniocervical region1.69e-0862
gallbladder4.45e-083
gall bladder primordium4.45e-083
anatomical space6.88e-0895
gingival epithelium7.25e-083
surface structure1.58e-0799
epithelium of mucosa2.97e-078
subdivision of digestive tract3.76e-07118
Disease
Ontology termp-valuen
carcinoma8.71e-10106
squamous cell carcinoma1.00e-0714


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
CEBPB#105147.971147625824820.0002476385788090830.00268484641671772
ELK4#2005416.2356816584681.43847748454449e-050.000343625686203893
FOS#235348.99795530889440.0001525147711168630.00195297819772855
GATA2#2624412.7449317335543.78864877853583e-050.000723898078634292
JUND#372735.245997956403270.01043432751748420.0387136570250642
STAT3#6774410.51946499715428.16377768286615e-050.00123370970542737
TBP#690843.706770687096390.005296377814784350.0244864277378602



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.