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Coexpression cluster:C3736: Difference between revisions

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|full_id=C3736_Keratinocyte_Mammary_salivary_Mallassezderived_Bronchial_keratoacanthoma_Gingival
|full_id=C3736_Keratinocyte_Mammary_salivary_Mallassezderived_Bronchial_keratoacanthoma_Gingival
|id=C3736
|id=C3736
|ontology_enrichment_celltype=CL:0000066!3.63e-33!254;CL:0002076!1.99e-22!43;CL:0000223!1.77e-15!59;CL:0002251!4.17e-11!21;CL:0002368!2.57e-10!13;CL:0002159!7.77e-09!13;CL:0000082!1.52e-08!19;CL:0002202!7.45e-07!9;CL:0002632!7.45e-07!9
|ontology_enrichment_celltype=CL:0000066!2.17e-34!253;CL:0002076!3.46e-28!42;CL:0000223!2.33e-21!58;CL:0002251!3.37e-18!20;CL:0002159!1.33e-13!14;CL:0002368!1.99e-12!13;CL:0000622!3.24e-11!5;CL:0000076!4.29e-10!63;CL:0000154!2.97e-09!6;CL:0002623!7.11e-08!3;CL:0002328!1.15e-07!3;CL:0002166!1.63e-07!3;CL:0002621!1.77e-07!3
|ontology_enrichment_disease=DOID:305!1.52e-25!106;DOID:0050687!4.61e-17!143;DOID:1749!2.19e-12!14;DOID:299!2.77e-08!25;DOID:162!5.87e-08!235;DOID:14566!1.23e-07!239
|ontology_enrichment_disease=DOID:1749!9.56e-23!14;DOID:305!1.74e-19!106;DOID:0050687!4.00e-14!143
|ontology_enrichment_uberon=UBERON:0001004!3.68e-28!72;UBERON:0004119!6.86e-27!169;UBERON:0000925!6.86e-27!169;UBERON:0006595!6.86e-27!169;UBERON:0000065!1.12e-21!53;UBERON:0001007!4.17e-20!155;UBERON:0001555!4.17e-20!155;UBERON:0007026!4.17e-20!155;UBERON:0000077!1.26e-18!130;UBERON:0000072!1.51e-18!46;UBERON:0004921!1.27e-17!129;UBERON:0004185!1.27e-17!129;UBERON:0008947!3.81e-17!38;UBERON:0003258!3.81e-17!38;UBERON:0001041!2.51e-14!98;UBERON:0005181!1.37e-11!35;UBERON:0005153!1.56e-11!37;UBERON:0000161!1.61e-11!35;UBERON:0005178!3.23e-11!34;UBERON:0002224!3.23e-11!34;UBERON:0000464!5.92e-11!104;UBERON:0000166!1.96e-09!21;UBERON:0004807!2.08e-09!28;UBERON:0005911!4.47e-09!82;UBERON:0001557!6.77e-09!19;UBERON:0000466!1.01e-08!126;UBERON:0001737!1.20e-08!9;UBERON:0004802!1.52e-08!19;UBERON:0000115!1.52e-08!19;UBERON:0002048!1.84e-08!22;UBERON:0000117!1.84e-08!22;UBERON:0000171!1.84e-08!22;UBERON:0000170!1.84e-08!22;UBERON:0005597!1.84e-08!22;UBERON:0000118!1.84e-08!22;UBERON:0005157!3.39e-08!51;UBERON:0005156!5.25e-08!59;UBERON:0000990!5.25e-08!59;UBERON:0004175!5.96e-08!25;UBERON:0000062!1.33e-07!511;UBERON:0000165!1.67e-07!28;UBERON:0000930!1.67e-07!28;UBERON:0000915!2.70e-07!52;UBERON:0005795!4.85e-07!22;UBERON:0003104!5.24e-07!238;UBERON:0009142!5.24e-07!238;UBERON:0003975!6.38e-07!22;UBERON:0000063!6.82e-07!97;UBERON:0003133!6.99e-07!48;UBERON:0003100!7.34e-07!41;UBERON:0005631!8.93e-07!14;UBERON:0000158!8.93e-07!14
|ontology_enrichment_uberon=UBERON:0001004!4.42e-23!74;UBERON:0004119!2.74e-19!160;UBERON:0000925!2.74e-19!160;UBERON:0006595!2.74e-19!160;UBERON:0000065!9.16e-17!54;UBERON:0001007!8.57e-15!145;UBERON:0001555!8.57e-15!145;UBERON:0007026!8.57e-15!145;UBERON:0000161!3.16e-14!36;UBERON:0000166!1.79e-13!22;UBERON:0000072!2.28e-13!47;UBERON:0001737!3.69e-13!9;UBERON:0001557!2.00e-12!19;UBERON:0004921!5.98e-12!118;UBERON:0003102!6.31e-12!99;UBERON:0001041!1.45e-11!87;UBERON:0008947!3.15e-11!38;UBERON:0003258!3.15e-11!38;UBERON:0000165!3.88e-11!29;UBERON:0000930!3.88e-11!29;UBERON:0000344!3.06e-10!20;UBERON:0003729!1.60e-09!13;UBERON:0003343!8.78e-09!4;UBERON:0004785!8.78e-09!4;UBERON:0000033!1.04e-08!56;UBERON:0000153!2.59e-08!62;UBERON:0007811!2.59e-08!62;UBERON:0004815!1.15e-07!3;UBERON:0002031!1.15e-07!3;UBERON:0001949!1.77e-07!3;UBERON:0000365!2.17e-07!5;UBERON:0001444!5.29e-07!49;UBERON:0001723!8.59e-07!3;UBERON:0001033!8.59e-07!3;UBERON:0010056!8.59e-07!3
|tf_chipseq_enrich=SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457442530225639
|tf_chipseq_enrich=SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457442530225639
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}}
}}

Revision as of 15:22, 19 October 2012


Full id: C3736_Keratinocyte_Mammary_salivary_Mallassezderived_Bronchial_keratoacanthoma_Gingival



Phase1 CAGE Peaks

Hg19::chr18:61144049..61144064,+p2@SERPINB5
Hg19::chr18:61144160..61144214,+p1@SERPINB5
Hg19::chr18:61171128..61171130,+p@chr18:61171128..61171130
+


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
respiratory system4.42e-2374
endoderm-derived structure2.74e-19160
endoderm2.74e-19160
presumptive endoderm2.74e-19160
respiratory tract9.16e-1754
digestive system8.57e-15145
digestive tract8.57e-15145
primitive gut8.57e-15145
orifice3.16e-1436
oral opening1.79e-1322
segment of respiratory tract2.28e-1347
larynx3.69e-139
upper respiratory tract2.00e-1219
subdivision of digestive tract5.98e-12118
surface structure6.31e-1299
foregut1.45e-1187
respiratory primordium3.15e-1138
endoderm of foregut3.15e-1138
mouth3.88e-1129
stomodeum3.88e-1129
mucosa3.06e-1020
mouth mucosa1.60e-0913
mucosa of oral region8.78e-094
respiratory system mucosa8.78e-094
head1.04e-0856
anterior region of body2.59e-0862
craniocervical region2.59e-0862
lower respiratory tract epithelium1.15e-073
epithelium of bronchus1.15e-073
gingival epithelium1.77e-073
urothelium2.17e-075
subdivision of head5.29e-0749
tongue8.59e-073
gustatory system8.59e-073
future tongue8.59e-073
Disease
Ontology termp-valuen
squamous cell carcinoma9.56e-2314
carcinoma1.74e-19106
cell type cancer4.00e-14143


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
SMC3#9126210.02995522995520.0126656379767470.0457442530225639



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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