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Coexpression cluster:C4088: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!1.10e-80!114;UBERON:0001049!8.46e-41!56;UBERON:0005068!8.46e-41!56;UBERON:0006241!8.46e-41!56;UBERON:0007135!8.46e-41!56;UBERON:0000073!9.37e-38!53;UBERON:0002616!9.37e-38!53;UBERON:0004111!2.54e-33!240;UBERON:0002780!7.36e-31!41;UBERON:0001890!7.36e-31!41;UBERON:0003080!7.36e-31!41;UBERON:0006240!7.36e-31!41;UBERON:0000025!1.75e-30!192;UBERON:0003075!9.31e-30!82;UBERON:0007284!9.31e-30!82;UBERON:0000477!1.73e-29!373;UBERON:0001017!3.68e-29!81;UBERON:0000955!1.43e-28!68;UBERON:0006238!1.43e-28!68;UBERON:0002346!1.49e-27!86;UBERON:0003528!3.73e-27!34;UBERON:0002020!3.73e-27!34;UBERON:0001893!1.57e-26!34;UBERON:0001016!5.00e-26!89;UBERON:0002791!9.20e-25!32;UBERON:0001869!2.10e-24!32;UBERON:0010314!1.25e-23!132;UBERON:0010371!1.17e-21!104;UBERON:0002619!7.18e-21!22;UBERON:0003056!1.30e-19!61;UBERON:0011216!3.43e-19!223;UBERON:0001950!1.16e-18!20;UBERON:0000483!2.52e-18!306;UBERON:0000119!7.37e-18!309;UBERON:0000956!1.26e-17!25;UBERON:0000203!1.26e-17!25;UBERON:0000481!5.51e-14!342;UBERON:0004638!1.20e-13!18;UBERON:0001986!1.20e-13!18;UBERON:0004852!1.20e-13!18;UBERON:0004121!4.38e-12!171;UBERON:0000924!4.38e-12!171;UBERON:0006601!4.38e-12!171;UBERON:0000468!2.07e-11!656;UBERON:0000125!2.19e-11!9;UBERON:0002308!2.19e-11!9;UBERON:0002420!2.37e-11!9;UBERON:0007245!2.37e-11!9;UBERON:0010009!2.37e-11!9;UBERON:0010011!2.37e-11!9;UBERON:0000454!2.37e-11!9;UBERON:0000467!3.65e-11!624;UBERON:0000480!4.42e-11!625;UBERON:0003076!7.20e-11!15;UBERON:0003057!7.20e-11!15;UBERON:0000064!2.54e-10!218;UBERON:0000487!2.54e-10!22;UBERON:0002050!1.93e-09!564;UBERON:0000923!2.41e-09!560;UBERON:0010316!2.41e-09!560;UBERON:0005291!2.41e-09!560;UBERON:0006598!2.41e-09!560;UBERON:0010317!2.41e-09!560;UBERON:0002532!2.41e-09!560;UBERON:0004732!2.84e-09!13;UBERON:0000922!5.60e-09!592;UBERON:0005423!6.08e-09!581;UBERON:0009663!6.31e-09!7;UBERON:0001871!1.05e-08!6;UBERON:0002298!1.25e-08!6;UBERON:0006914!1.49e-08!25;UBERON:0000062!3.00e-08!503;UBERON:0002465!4.20e-08!10;UBERON:0004733!4.49e-08!12;UBERON:0002028!4.49e-08!12;UBERON:0007277!4.49e-08!12;UBERON:0000055!6.39e-08!68;UBERON:0000200!2.95e-07!6;UBERON:0001638!4.68e-07!9;UBERON:0003920!4.68e-07!9;UBERON:0004582!4.68e-07!9;UBERON:0000349!5.45e-07!5
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}}
}}

Revision as of 16:32, 26 November 2012


Full id: C4088_Hepatic_Endothelial_Renal_adipose_Lymphatic_breast_lung



Phase1 CAGE Peaks

Hg19::chr22:19511923..19511939,-p1@CLDN5
Hg19::chr22:19512824..19512885,-p2@CLDN5
Hg19::chr22:19512893..19512908,-p3@CLDN5


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 organism1.10e-80114
neural tube8.46e-4156
neural rod8.46e-4156
future spinal cord8.46e-4156
neural keel8.46e-4156
regional part of nervous system9.37e-3853
regional part of brain9.37e-3853
anatomical conduit2.54e-33240
regional part of forebrain7.36e-3141
forebrain7.36e-3141
anterior neural tube7.36e-3141
future forebrain7.36e-3141
tube1.75e-30192
neural plate9.31e-3082
presumptive neural plate9.31e-3082
anatomical cluster1.73e-29373
central nervous system3.68e-2981
brain1.43e-2868
future brain1.43e-2868
neurectoderm1.49e-2786
brain grey matter3.73e-2734
gray matter3.73e-2734
telencephalon1.57e-2634
nervous system5.00e-2689
regional part of telencephalon9.20e-2532
cerebral hemisphere2.10e-2432
structure with developmental contribution from neural crest1.25e-23132
ecto-epithelium1.17e-21104
regional part of cerebral cortex7.18e-2122
pre-chordal neural plate1.30e-1961
organ system subdivision3.43e-19223
neocortex1.16e-1820
epithelium2.52e-18306
cell layer7.37e-18309
cerebral cortex1.26e-1725
pallium1.26e-1725
multi-tissue structure5.51e-14342
blood vessel endothelium1.20e-1318
endothelium1.20e-1318
cardiovascular system endothelium1.20e-1318
ectoderm-derived structure4.38e-12171
ectoderm4.38e-12171
presumptive ectoderm4.38e-12171
multi-cellular organism2.07e-11656
neural nucleus2.19e-119
nucleus of brain2.19e-119
basal ganglion2.37e-119
nuclear complex of neuraxis2.37e-119
aggregate regional part of brain2.37e-119
collection of basal ganglia2.37e-119
cerebral subcortex2.37e-119
anatomical system3.65e-11624
anatomical group4.42e-11625
posterior neural tube7.20e-1115
chordal neural plate7.20e-1115
organ part2.54e-10218
simple squamous epithelium2.54e-1022
embryonic structure1.93e-09564
germ layer2.41e-09560
germ layer / neural crest2.41e-09560
embryonic tissue2.41e-09560
presumptive structure2.41e-09560
germ layer / neural crest derived structure2.41e-09560
epiblast (generic)2.41e-09560
segmental subdivision of nervous system2.84e-0913
embryo5.60e-09592
developing anatomical structure6.08e-09581
telencephalic nucleus6.31e-097
temporal lobe1.05e-086
brainstem1.25e-086
squamous epithelium1.49e-0825
organ3.00e-08503
lymphoid system4.20e-0810
segmental subdivision of hindbrain4.49e-0812
hindbrain4.49e-0812
presumptive hindbrain4.49e-0812
vessel6.39e-0868
gyrus2.95e-076
vein4.68e-079
venous blood vessel4.68e-079
venous system4.68e-079
limbic system5.45e-075


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

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.

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