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Coexpression cluster:C2925: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.75e-38!115;UBERON:0000477!3.77e-22!286;UBERON:0004111!1.96e-18!241;UBERON:0000481!6.87e-18!347;UBERON:0001049!6.70e-16!57;UBERON:0005068!6.70e-16!57;UBERON:0006241!6.70e-16!57;UBERON:0007135!6.70e-16!57;UBERON:0002346!6.86e-16!90;UBERON:0000468!2.08e-15!659;UBERON:0003075!4.99e-15!86;UBERON:0007284!4.99e-15!86;UBERON:0002616!6.82e-15!59;UBERON:0000119!1.52e-14!312;UBERON:0000483!3.84e-14!309;UBERON:0000025!7.84e-14!194;UBERON:0000467!1.42e-13!625;UBERON:0000480!2.61e-13!626;UBERON:0002020!4.20e-13!34;UBERON:0003528!4.20e-13!34;UBERON:0001893!5.00e-13!34;UBERON:0002791!1.37e-12!33;UBERON:0003080!2.21e-12!42;UBERON:0002780!2.32e-12!41;UBERON:0001890!2.32e-12!41;UBERON:0006240!2.32e-12!41;UBERON:0005743!5.78e-12!86;UBERON:0000033!6.07e-12!123;UBERON:0000922!7.38e-12!612;UBERON:0001869!9.11e-12!32;UBERON:0000073!1.57e-11!94;UBERON:0001016!1.57e-11!94;UBERON:0000955!1.63e-11!69;UBERON:0006238!1.63e-11!69;UBERON:0000153!2.67e-11!129;UBERON:0007811!2.67e-11!129;UBERON:0002050!6.47e-11!605;UBERON:0005423!6.47e-11!605;UBERON:0001017!6.72e-11!82;UBERON:0000475!8.65e-11!365;UBERON:0000923!1.24e-10!604;UBERON:0005291!1.24e-10!604;UBERON:0006598!1.24e-10!604;UBERON:0002532!1.24e-10!604;UBERON:0003056!1.47e-10!61;UBERON:0000064!1.97e-10!219;UBERON:0000924!8.68e-10!173;UBERON:0006601!8.68e-10!173;UBERON:0001986!1.90e-09!18;UBERON:0004638!1.90e-09!18;UBERON:0004852!1.90e-09!18;UBERON:0004121!4.08e-09!169;UBERON:0000956!2.05e-08!25;UBERON:0000203!2.05e-08!25;UBERON:0000062!2.30e-08!511;UBERON:0002619!3.23e-08!22;UBERON:0004921!1.12e-07!129;UBERON:0004185!1.12e-07!129;UBERON:0001007!1.53e-07!155;UBERON:0001555!1.53e-07!155;UBERON:0007026!1.53e-07!155;UBERON:0001950!1.78e-07!20;UBERON:0000487!1.93e-07!22;UBERON:0006914!4.12e-07!25
|ontology_enrichment_uberon=UBERON:0007023!2.75e-38!115;UBERON:0000477!3.77e-22!286;UBERON:0004111!1.96e-18!241;UBERON:0000481!6.87e-18!347;UBERON:0001049!6.70e-16!57;UBERON:0005068!6.70e-16!57;UBERON:0006241!6.70e-16!57;UBERON:0007135!6.70e-16!57;UBERON:0002346!6.86e-16!90;UBERON:0000468!2.08e-15!659;UBERON:0003075!4.99e-15!86;UBERON:0007284!4.99e-15!86;UBERON:0002616!6.82e-15!59;UBERON:0000119!1.52e-14!312;UBERON:0000483!3.84e-14!309;UBERON:0000025!7.84e-14!194;UBERON:0000467!1.42e-13!625;UBERON:0000480!2.61e-13!626;UBERON:0002020!4.20e-13!34;UBERON:0003528!4.20e-13!34;UBERON:0001893!5.00e-13!34;UBERON:0002791!1.37e-12!33;UBERON:0003080!2.21e-12!42;UBERON:0002780!2.32e-12!41;UBERON:0001890!2.32e-12!41;UBERON:0006240!2.32e-12!41;UBERON:0005743!5.78e-12!86;UBERON:0000033!6.07e-12!123;UBERON:0000922!7.38e-12!612;UBERON:0001869!9.11e-12!32;UBERON:0000073!1.57e-11!94;UBERON:0001016!1.57e-11!94;UBERON:0000955!1.63e-11!69;UBERON:0006238!1.63e-11!69;UBERON:0000153!2.67e-11!129;UBERON:0007811!2.67e-11!129;UBERON:0002050!6.47e-11!605;UBERON:0005423!6.47e-11!605;UBERON:0001017!6.72e-11!82;UBERON:0000475!8.65e-11!365;UBERON:0000923!1.24e-10!604;UBERON:0005291!1.24e-10!604;UBERON:0006598!1.24e-10!604;UBERON:0002532!1.24e-10!604;UBERON:0003056!1.47e-10!61;UBERON:0000064!1.97e-10!219;UBERON:0000924!8.68e-10!173;UBERON:0006601!8.68e-10!173;UBERON:0001986!1.90e-09!18;UBERON:0004638!1.90e-09!18;UBERON:0004852!1.90e-09!18;UBERON:0004121!4.08e-09!169;UBERON:0000956!2.05e-08!25;UBERON:0000203!2.05e-08!25;UBERON:0000062!2.30e-08!511;UBERON:0002619!3.23e-08!22;UBERON:0004921!1.12e-07!129;UBERON:0004185!1.12e-07!129;UBERON:0001007!1.53e-07!155;UBERON:0001555!1.53e-07!155;UBERON:0007026!1.53e-07!155;UBERON:0001950!1.78e-07!20;UBERON:0000487!1.93e-07!22;UBERON:0006914!4.12e-07!25
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820303583096487!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106851326912651!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240651803821917!HNF4A#3172;4:23.1322903629537:3.48990320893214e-06:0.000115966274654045
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}}
}}

Revision as of 13:46, 5 September 2012


Full id: C2925_optic_smooth_colon_corpus_globus_thalamus_ductus



Phase1 CAGE Peaks

Hg19::chr8:38614412..38614456,+p7@TACC1
Hg19::chr8:38614754..38614774,+p13@TACC1
Hg19::chr8:38614778..38614806,+p5@TACC1
Hg19::chr8:38614807..38614824,+p10@TACC1


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><br>


Uber Anatomy
Ontology termp-valuen
adult organism2.75e-38115
anatomical cluster3.77e-22286
anatomical conduit1.96e-18241
multi-tissue structure6.87e-18347
neural tube6.70e-1657
neural rod6.70e-1657
future spinal cord6.70e-1657
neural keel6.70e-1657
neurectoderm6.86e-1690
multi-cellular organism2.08e-15659
neural plate4.99e-1586
presumptive neural plate4.99e-1586
regional part of brain6.82e-1559
cell layer1.52e-14312
epithelium3.84e-14309
tube7.84e-14194
anatomical system1.42e-13625
anatomical group2.61e-13626
gray matter4.20e-1334
brain grey matter4.20e-1334
telencephalon5.00e-1334
regional part of telencephalon1.37e-1233
anterior neural tube2.21e-1242
regional part of forebrain2.32e-1241
forebrain2.32e-1241
future forebrain2.32e-1241
head6.07e-12123
embryo7.38e-12612
cerebral hemisphere9.11e-1232
regional part of nervous system1.57e-1194
nervous system1.57e-1194
brain1.63e-1169
future brain1.63e-1169
anterior region of body2.67e-11129
craniocervical region2.67e-11129
embryonic structure6.47e-11605
developing anatomical structure6.47e-11605
central nervous system6.72e-1182
organism subdivision8.65e-11365
germ layer1.24e-10604
embryonic tissue1.24e-10604
presumptive structure1.24e-10604
epiblast (generic)1.24e-10604
pre-chordal neural plate1.47e-1061
organ part1.97e-10219
ectoderm8.68e-10173
presumptive ectoderm8.68e-10173
endothelium1.90e-0918
blood vessel endothelium1.90e-0918
cardiovascular system endothelium1.90e-0918
ectoderm-derived structure4.08e-09169
cerebral cortex2.05e-0825
pallium2.05e-0825
organ2.30e-08511
regional part of cerebral cortex3.23e-0822
subdivision of digestive tract1.12e-07129
endodermal part of digestive tract1.12e-07129
digestive system1.53e-07155
digestive tract1.53e-07155
primitive gut1.53e-07155
neocortex1.78e-0720
simple squamous epithelium1.93e-0722
squamous epithelium4.12e-0725


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
CTCF#1066445.360256373075030.001211145381643620.00820303583096487
E2F1#186944.907389214879320.001724022357361790.0106851326912651
EBF1#187936.679850134926750.005184294118278910.0240651803821917
HNF4A#3172423.13229036295373.48990320893214e-060.000115966274654045



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.