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Coexpression cluster:C1040: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.43e-39!115;UBERON:0000477!1.59e-23!286;UBERON:0004111!4.60e-23!241;UBERON:0000025!2.35e-20!194;UBERON:0003075!1.00e-19!86;UBERON:0007284!1.00e-19!86;UBERON:0001049!1.98e-19!57;UBERON:0005068!1.98e-19!57;UBERON:0006241!1.98e-19!57;UBERON:0007135!1.98e-19!57;UBERON:0000483!1.16e-18!309;UBERON:0000119!2.11e-18!312;UBERON:0002616!8.60e-18!59;UBERON:0002346!1.66e-17!90;UBERON:0005743!1.11e-15!86;UBERON:0000073!2.03e-15!94;UBERON:0001016!2.03e-15!94;UBERON:0000481!4.96e-15!347;UBERON:0000468!5.52e-15!659;UBERON:0001017!1.25e-14!82;UBERON:0003080!1.47e-14!42;UBERON:0000955!2.21e-14!69;UBERON:0006238!2.21e-14!69;UBERON:0002780!5.27e-14!41;UBERON:0001890!5.27e-14!41;UBERON:0006240!5.27e-14!41;UBERON:0003056!2.51e-13!61;UBERON:0000153!4.43e-12!129;UBERON:0007811!4.43e-12!129;UBERON:0000475!7.23e-12!365;UBERON:0000467!9.20e-12!625;UBERON:0001893!1.08e-11!34;UBERON:0000480!1.22e-11!626;UBERON:0002020!1.93e-11!34;UBERON:0003528!1.93e-11!34;UBERON:0002791!2.86e-11!33;UBERON:0000033!5.66e-11!123;UBERON:0001869!6.63e-11!32;UBERON:0003103!8.74e-10!69;UBERON:0004121!1.29e-09!169;UBERON:0000922!5.07e-09!612;UBERON:0000064!8.72e-09!219;UBERON:0000062!1.01e-08!511;UBERON:0000924!1.07e-08!173;UBERON:0006601!1.07e-08!173;UBERON:0000956!2.24e-08!25;UBERON:0000203!2.24e-08!25;UBERON:0003914!2.87e-08!118;UBERON:0002050!3.01e-08!605;UBERON:0005423!3.01e-08!605;UBERON:0002619!3.90e-08!22;UBERON:0000923!5.98e-08!604;UBERON:0005291!5.98e-08!604;UBERON:0006598!5.98e-08!604;UBERON:0002532!5.98e-08!604;UBERON:0001950!1.01e-07!20;UBERON:0004872!2.41e-07!84;UBERON:0007100!8.91e-07!27
|ontology_enrichment_uberon=UBERON:0007023!3.34e-55!114;UBERON:0001049!6.78e-19!56;UBERON:0005068!6.78e-19!56;UBERON:0006241!6.78e-19!56;UBERON:0007135!6.78e-19!56;UBERON:0003075!6.21e-17!82;UBERON:0007284!6.21e-17!82;UBERON:0000073!6.66e-17!53;UBERON:0002616!6.66e-17!53;UBERON:0000477!1.41e-16!373;UBERON:0002346!2.12e-15!86;UBERON:0001017!7.32e-15!81;UBERON:0000481!1.42e-14!342;UBERON:0010314!1.70e-14!132;UBERON:0000955!2.75e-14!68;UBERON:0006238!2.75e-14!68;UBERON:0011216!1.47e-13!223;UBERON:0001893!5.61e-13!34;UBERON:0002780!1.29e-12!41;UBERON:0001890!1.29e-12!41;UBERON:0003080!1.29e-12!41;UBERON:0006240!1.29e-12!41;UBERON:0003528!1.55e-12!34;UBERON:0002020!1.55e-12!34;UBERON:0001016!1.58e-12!89;UBERON:0001869!7.70e-12!32;UBERON:0002791!1.25e-11!32;UBERON:0004111!3.36e-11!240;UBERON:0010371!6.97e-11!104;UBERON:0003056!2.75e-10!61;UBERON:0000956!4.78e-10!25;UBERON:0000203!4.78e-10!25;UBERON:0000468!1.94e-09!656;UBERON:0000062!2.07e-09!503;UBERON:0000025!4.96e-09!192;UBERON:0000483!7.43e-09!306;UBERON:0002619!1.07e-08!22;UBERON:0001950!1.26e-08!20;UBERON:0000119!1.61e-08!309;UBERON:0003076!9.46e-08!15;UBERON:0003057!9.46e-08!15;UBERON:0000467!1.36e-07!624;UBERON:0004121!1.56e-07!171;UBERON:0000924!1.56e-07!171;UBERON:0006601!1.56e-07!171;UBERON:0000480!1.66e-07!625;UBERON:0000922!1.94e-07!592;UBERON:0000064!3.54e-07!218;UBERON:0005423!5.88e-07!581
|tf_chipseq_enrich=CTBP2#1488;3:23.518875127248:0.000213570629447747:0.00246166018859875
|tf_chipseq_enrich=CTBP2#1488;3:23.518875127248:0.000213570629447747:0.00246166018859875
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}}
}}

Revision as of 10:44, 19 October 2012


Full id: C1040_smooth_aorta_heart_bladder_uterus_penis_cervix



Phase1 CAGE Peaks

Hg19::chr14:94443066..94443092,-p2@ASB2
Hg19::chr2:218843537..218843559,-p4@TNS1
Hg19::chr2:218843565..218843592,-p8@TNS1
Hg19::chr2:218843623..218843635,-p11@TNS1
Hg19::chr4:119809984..119810024,+p2@SYNPO2
Hg19::chr4:119810034..119810045,+p8@SYNPO2
Hg19::chr9:70971821..70971841,+p2@PGM5
Hg19::chrX:11683221..11683257,-p3@ARHGAP6


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:0004614phosphoglucomutase activity0.0234374204859477
GO:0004252serine-type endopeptidase activity0.0234374204859477
GO:0008236serine-type peptidase activity0.0234374204859477
GO:0017171serine hydrolase activity0.0234374204859477
GO:0030054cell junction0.0234374204859477
GO:0003779actin binding0.0234374204859477
GO:0005913cell-cell adherens junction0.0237632929688061
GO:0008092cytoskeletal protein binding0.0254837298998518
GO:0044267cellular protein metabolic process0.0254837298998518
GO:0044260cellular macromolecule metabolic process0.0254837298998518
GO:0005100Rho GTPase activator activity0.0254837298998518
GO:0005884actin filament0.0254837298998518
GO:0019538protein metabolic process0.0254837298998518
GO:0016868intramolecular transferase activity, phosphotransferases0.0264162701651135
GO:0030041actin filament polymerization0.0264162701651135
GO:0004289subtilase activity0.0272350536668043
GO:0004175endopeptidase activity0.0272350536668043
GO:0005070SH3/SH2 adaptor activity0.0347587692753149
GO:0005912adherens junction0.0362788179553529
GO:0060090molecular adaptor activity0.0370633375511242
GO:0008154actin polymerization and/or depolymerization0.0370633375511242
GO:0016866intramolecular transferase activity0.0394222340296126
GO:0008233peptidase activity0.0465675100398205
GO:0030674protein binding, bridging0.0475019981986934
GO:0006508proteolysis0.0475019981986934
GO:0051258protein polymerization0.0475019981986934



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><br>


Uber Anatomy
Ontology termp-valuen
adult organism3.34e-55114
neural tube6.78e-1956
neural rod6.78e-1956
future spinal cord6.78e-1956
neural keel6.78e-1956
neural plate6.21e-1782
presumptive neural plate6.21e-1782
regional part of nervous system6.66e-1753
regional part of brain6.66e-1753
anatomical cluster1.41e-16373
neurectoderm2.12e-1586
central nervous system7.32e-1581
multi-tissue structure1.42e-14342
structure with developmental contribution from neural crest1.70e-14132
brain2.75e-1468
future brain2.75e-1468
organ system subdivision1.47e-13223
telencephalon5.61e-1334
regional part of forebrain1.29e-1241
forebrain1.29e-1241
anterior neural tube1.29e-1241
future forebrain1.29e-1241
brain grey matter1.55e-1234
gray matter1.55e-1234
nervous system1.58e-1289
cerebral hemisphere7.70e-1232
regional part of telencephalon1.25e-1132
anatomical conduit3.36e-11240
ecto-epithelium6.97e-11104
pre-chordal neural plate2.75e-1061
cerebral cortex4.78e-1025
pallium4.78e-1025
multi-cellular organism1.94e-09656
organ2.07e-09503
tube4.96e-09192
epithelium7.43e-09306
regional part of cerebral cortex1.07e-0822
neocortex1.26e-0820
cell layer1.61e-08309
posterior neural tube9.46e-0815
chordal neural plate9.46e-0815
anatomical system1.36e-07624
ectoderm-derived structure1.56e-07171
ectoderm1.56e-07171
presumptive ectoderm1.56e-07171
anatomical group1.66e-07625
embryo1.94e-07592
organ part3.54e-07218
developing anatomical structure5.88e-07581


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
CTBP2#1488323.5188751272480.0002135706294477470.00246166018859875



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.