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Coexpression cluster:C2633: Difference between revisions

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|ontology_enrichment_disease=DOID:305!2.23e-19!106;DOID:0050687!1.86e-12!143;DOID:299!2.06e-09!25;DOID:162!5.40e-09!235;DOID:14566!2.06e-08!239
|ontology_enrichment_disease=DOID:305!2.23e-19!106;DOID:0050687!1.86e-12!143;DOID:299!2.06e-09!25;DOID:162!5.40e-09!235;DOID:14566!2.06e-08!239
|ontology_enrichment_uberon=UBERON:0007023!3.37e-34!115;UBERON:0001049!1.34e-24!57;UBERON:0005068!1.34e-24!57;UBERON:0006241!1.34e-24!57;UBERON:0007135!1.34e-24!57;UBERON:0002616!5.58e-21!59;UBERON:0000955!1.21e-19!69;UBERON:0006238!1.21e-19!69;UBERON:0003080!2.57e-19!42;UBERON:0002780!1.22e-18!41;UBERON:0001890!1.22e-18!41;UBERON:0006240!1.22e-18!41;UBERON:0001017!1.06e-17!82;UBERON:0005743!3.04e-17!86;UBERON:0002020!2.34e-16!34;UBERON:0003528!2.34e-16!34;UBERON:0003075!3.65e-16!86;UBERON:0007284!3.65e-16!86;UBERON:0001869!7.46e-15!32;UBERON:0002346!8.12e-15!90;UBERON:0001893!9.19e-15!34;UBERON:0000073!2.92e-14!94;UBERON:0001016!2.92e-14!94;UBERON:0002791!5.21e-14!33;UBERON:0000153!3.03e-13!129;UBERON:0007811!3.03e-13!129;UBERON:0001737!3.50e-13!9;UBERON:0003056!4.11e-12!61;UBERON:0000033!8.77e-12!123;UBERON:0002619!4.97e-11!22;UBERON:0001950!6.85e-11!20;UBERON:0000064!2.54e-10!219;UBERON:0002420!7.53e-10!9;UBERON:0007245!7.53e-10!9;UBERON:0010009!7.53e-10!9;UBERON:0010011!7.53e-10!9;UBERON:0000454!7.53e-10!9;UBERON:0002308!7.97e-10!9;UBERON:0000125!7.97e-10!9;UBERON:0000477!1.06e-09!286;UBERON:0000956!3.61e-09!25;UBERON:0000203!3.61e-09!25;UBERON:0001557!3.92e-09!19;UBERON:0001041!8.65e-09!98;UBERON:0002294!1.89e-08!7;UBERON:0001173!1.89e-08!7;UBERON:0004912!1.89e-08!7;UBERON:0000481!3.03e-08!347;UBERON:0002298!4.19e-08!8;UBERON:0009663!5.82e-08!7;UBERON:0001007!6.53e-08!155;UBERON:0001555!6.53e-08!155;UBERON:0007026!6.53e-08!155;UBERON:0000077!7.45e-08!130;UBERON:0000062!9.07e-08!511;UBERON:0008947!2.79e-07!38;UBERON:0003258!2.79e-07!38;UBERON:0000200!3.38e-07!6;UBERON:0004921!5.09e-07!129;UBERON:0004185!5.09e-07!129;UBERON:0004119!5.19e-07!169;UBERON:0000925!5.19e-07!169;UBERON:0006595!5.19e-07!169
|ontology_enrichment_uberon=UBERON:0007023!3.37e-34!115;UBERON:0001049!1.34e-24!57;UBERON:0005068!1.34e-24!57;UBERON:0006241!1.34e-24!57;UBERON:0007135!1.34e-24!57;UBERON:0002616!5.58e-21!59;UBERON:0000955!1.21e-19!69;UBERON:0006238!1.21e-19!69;UBERON:0003080!2.57e-19!42;UBERON:0002780!1.22e-18!41;UBERON:0001890!1.22e-18!41;UBERON:0006240!1.22e-18!41;UBERON:0001017!1.06e-17!82;UBERON:0005743!3.04e-17!86;UBERON:0002020!2.34e-16!34;UBERON:0003528!2.34e-16!34;UBERON:0003075!3.65e-16!86;UBERON:0007284!3.65e-16!86;UBERON:0001869!7.46e-15!32;UBERON:0002346!8.12e-15!90;UBERON:0001893!9.19e-15!34;UBERON:0000073!2.92e-14!94;UBERON:0001016!2.92e-14!94;UBERON:0002791!5.21e-14!33;UBERON:0000153!3.03e-13!129;UBERON:0007811!3.03e-13!129;UBERON:0001737!3.50e-13!9;UBERON:0003056!4.11e-12!61;UBERON:0000033!8.77e-12!123;UBERON:0002619!4.97e-11!22;UBERON:0001950!6.85e-11!20;UBERON:0000064!2.54e-10!219;UBERON:0002420!7.53e-10!9;UBERON:0007245!7.53e-10!9;UBERON:0010009!7.53e-10!9;UBERON:0010011!7.53e-10!9;UBERON:0000454!7.53e-10!9;UBERON:0002308!7.97e-10!9;UBERON:0000125!7.97e-10!9;UBERON:0000477!1.06e-09!286;UBERON:0000956!3.61e-09!25;UBERON:0000203!3.61e-09!25;UBERON:0001557!3.92e-09!19;UBERON:0001041!8.65e-09!98;UBERON:0002294!1.89e-08!7;UBERON:0001173!1.89e-08!7;UBERON:0004912!1.89e-08!7;UBERON:0000481!3.03e-08!347;UBERON:0002298!4.19e-08!8;UBERON:0009663!5.82e-08!7;UBERON:0001007!6.53e-08!155;UBERON:0001555!6.53e-08!155;UBERON:0007026!6.53e-08!155;UBERON:0000077!7.45e-08!130;UBERON:0000062!9.07e-08!511;UBERON:0008947!2.79e-07!38;UBERON:0003258!2.79e-07!38;UBERON:0000200!3.38e-07!6;UBERON:0004921!5.09e-07!129;UBERON:0004185!5.09e-07!129;UBERON:0004119!5.19e-07!169;UBERON:0000925!5.19e-07!169;UBERON:0006595!5.19e-07!169
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}}
}}

Revision as of 18:28, 8 August 2012


Full id: C2633_smallcell_Hep2_gall_cervical_splenic_mesothelioma_serous



Phase1 CAGE Peaks

Hg19::chr21:43816105..43816116,-p3@TMPRSS3
Hg19::chr21:43816124..43816151,-p2@TMPRSS3
Hg19::chr21:43816152..43816182,-p1@TMPRSS3
Hg19::chr21:43816226..43816231,-p4@TMPRSS3


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism3.37e-34115
neural tube1.34e-2457
neural rod1.34e-2457
future spinal cord1.34e-2457
neural keel1.34e-2457
regional part of brain5.58e-2159
brain1.21e-1969
future brain1.21e-1969
anterior neural tube2.57e-1942
regional part of forebrain1.22e-1841
forebrain1.22e-1841
future forebrain1.22e-1841
central nervous system1.06e-1782
gray matter2.34e-1634
brain grey matter2.34e-1634
neural plate3.65e-1686
presumptive neural plate3.65e-1686
cerebral hemisphere7.46e-1532
neurectoderm8.12e-1590
telencephalon9.19e-1534
regional part of nervous system2.92e-1494
nervous system2.92e-1494
regional part of telencephalon5.21e-1433
anterior region of body3.03e-13129
craniocervical region3.03e-13129
larynx3.50e-139
pre-chordal neural plate4.11e-1261
head8.77e-12123
regional part of cerebral cortex4.97e-1122
neocortex6.85e-1120
organ part2.54e-10219
basal ganglion7.53e-109
nuclear complex of neuraxis7.53e-109
aggregate regional part of brain7.53e-109
collection of basal ganglia7.53e-109
cerebral subcortex7.53e-109
nucleus of brain7.97e-109
neural nucleus7.97e-109
anatomical cluster1.06e-09286
cerebral cortex3.61e-0925
pallium3.61e-0925
upper respiratory tract3.92e-0919
foregut8.65e-0998
biliary system1.89e-087
biliary tree1.89e-087
biliary bud1.89e-087
multi-tissue structure3.03e-08347
brainstem4.19e-088
telencephalic nucleus5.82e-087
digestive system6.53e-08155
digestive tract6.53e-08155
primitive gut6.53e-08155
mixed endoderm/mesoderm-derived structure7.45e-08130
organ9.07e-08511
respiratory primordium2.79e-0738
endoderm of foregut2.79e-0738
gyrus3.38e-076
subdivision of digestive tract5.09e-07129
endodermal part of digestive tract5.09e-07129
endoderm-derived structure5.19e-07169
endoderm5.19e-07169
presumptive endoderm5.19e-07169
Disease
Ontology termp-valuen
carcinoma2.23e-19106
cell type cancer1.86e-12143
adenocarcinoma2.06e-0925
cancer5.40e-09235
disease of cellular proliferation2.06e-08239


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)

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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


No analysis results for this cluster

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.