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Coexpression cluster:C2720: Difference between revisions

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|ontology_enrichment_disease=DOID:305!2.37e-09!106;DOID:0050687!6.10e-08!143
|ontology_enrichment_disease=DOID:305!2.37e-09!106;DOID:0050687!6.10e-08!143
|ontology_enrichment_uberon=UBERON:0003102!9.18e-25!95;UBERON:0004119!7.51e-17!169;UBERON:0000925!7.51e-17!169;UBERON:0006595!7.51e-17!169;UBERON:0001004!7.10e-14!72;UBERON:0001007!1.13e-12!155;UBERON:0001555!1.13e-12!155;UBERON:0007026!1.13e-12!155;UBERON:0002097!3.33e-12!40;UBERON:0002199!4.01e-12!45;UBERON:0002416!4.01e-12!45;UBERON:0000161!7.07e-11!35;UBERON:0000077!1.53e-10!130;UBERON:0000065!2.39e-09!53;UBERON:0004921!7.14e-09!129;UBERON:0004185!7.14e-09!129;UBERON:0004923!1.19e-08!57;UBERON:0003104!1.42e-08!238;UBERON:0009142!1.42e-08!238;UBERON:0000165!1.16e-07!28;UBERON:0000930!1.16e-07!28;UBERON:0000166!1.23e-07!21;UBERON:0001041!1.43e-07!98;UBERON:0000072!1.71e-07!46;UBERON:0001737!7.15e-07!9;UBERON:0001557!8.47e-07!19
|ontology_enrichment_uberon=UBERON:0003102!9.18e-25!95;UBERON:0004119!7.51e-17!169;UBERON:0000925!7.51e-17!169;UBERON:0006595!7.51e-17!169;UBERON:0001004!7.10e-14!72;UBERON:0001007!1.13e-12!155;UBERON:0001555!1.13e-12!155;UBERON:0007026!1.13e-12!155;UBERON:0002097!3.33e-12!40;UBERON:0002199!4.01e-12!45;UBERON:0002416!4.01e-12!45;UBERON:0000161!7.07e-11!35;UBERON:0000077!1.53e-10!130;UBERON:0000065!2.39e-09!53;UBERON:0004921!7.14e-09!129;UBERON:0004185!7.14e-09!129;UBERON:0004923!1.19e-08!57;UBERON:0003104!1.42e-08!238;UBERON:0009142!1.42e-08!238;UBERON:0000165!1.16e-07!28;UBERON:0000930!1.16e-07!28;UBERON:0000166!1.23e-07!21;UBERON:0001041!1.43e-07!98;UBERON:0000072!1.71e-07!46;UBERON:0001737!7.15e-07!9;UBERON:0001557!8.47e-07!19
|tf_chipseq_enrich=ATF3#467;4:22.4631745260087:3.92475754624726e-06:0.000127535081945401!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268345357255051!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.000728045418124931!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434754444894931!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000718915285440686!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000744139858872045!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392147806766942!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129707362183275!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000827519363100827!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000438933292973858!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123335278087785!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322857333419123!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244712618385358!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000682067215312925
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}}
}}

Revision as of 14:22, 5 September 2012


Full id: C2720_salivary_cervical_epidermoid_malignant_Keratinocyte_Small_Sebocyte



Phase1 CAGE Peaks

Hg19::chr3:136676792..136676810,+p2@IL20RB
Hg19::chr3:136676818..136676840,+p1@IL20RB
Hg19::chr3:136676853..136676864,+p3@IL20RB
Hg19::chr3:136676869..136676878,+p4@IL20RB


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>

Cell Type
Ontology termp-valuen
epithelial cell8.01e-15254
endo-epithelial cell1.26e-1443
fibroblast3.64e-1275
endodermal cell2.25e-1159
epithelial cell of alimentary canal2.52e-1021
skin fibroblast1.30e-0823
animal cell4.69e-08679
eukaryotic cell4.69e-08679
general ecto-epithelial cell9.09e-0713
Uber Anatomy
Ontology termp-valuen
surface structure9.18e-2595
endoderm-derived structure7.51e-17169
endoderm7.51e-17169
presumptive endoderm7.51e-17169
respiratory system7.10e-1472
digestive system1.13e-12155
digestive tract1.13e-12155
primitive gut1.13e-12155
skin of body3.33e-1240
integument4.01e-1245
integumental system4.01e-1245
orifice7.07e-1135
mixed endoderm/mesoderm-derived structure1.53e-10130
respiratory tract2.39e-0953
subdivision of digestive tract7.14e-09129
endodermal part of digestive tract7.14e-09129
organ component layer1.19e-0857
mesenchyme1.42e-08238
entire embryonic mesenchyme1.42e-08238
mouth1.16e-0728
stomodeum1.16e-0728
oral opening1.23e-0721
foregut1.43e-0798
segment of respiratory tract1.71e-0746
larynx7.15e-079
upper respiratory tract8.47e-0719
Disease
Ontology termp-valuen
carcinoma2.37e-09106
cell type cancer6.10e-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
ATF3#467422.46317452600873.92475754624726e-060.000127535081945401
CEBPB#105147.971147625824820.0002476385788090830.00268345357255051
E2F4#1874412.66806031528443.88145892637771e-050.000728045418124931
EP300#203346.77394172622320.0004748459821442640.00434754444894931
GTF2F1#2962412.73966087675773.79492332235515e-050.000718915285440686
JUN#3725412.51282919233634.07770316866756e-050.000744139858872045
JUND#372746.994663941871030.000417684217818580.00392147806766942
RAD21#5885410.35503389545638.6948481184721e-050.00129707362183275
RFX5#5993412.04791082719514.74457429336527e-050.000827519363100827
SMC3#9126415.04493284493281.95092670935632e-050.000438933292973858
STAT3#6774410.51946499715428.16377768286615e-050.00123335278087785
TAF1#687243.343046285745290.008005664898701650.0322857333419123
TBP#690843.706770687096390.005296377814784350.0244712618385358
USF2#7392412.99219738506963.50833029870167e-050.000682067215312925



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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