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Coexpression cluster:C4088: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.66e-61!115;UBERON:0001049!2.96e-30!57;UBERON:0005068!2.96e-30!57;UBERON:0006241!2.96e-30!57;UBERON:0007135!2.96e-30!57;UBERON:0002616!2.47e-27!59;UBERON:0005743!1.70e-26!86;UBERON:0001017!1.86e-26!82;UBERON:0003075!3.41e-24!86;UBERON:0007284!3.41e-24!86;UBERON:0004111!3.59e-24!241;UBERON:0000073!7.18e-24!94;UBERON:0001016!7.18e-24!94;UBERON:0002346!7.59e-24!90;UBERON:0000955!1.26e-23!69;UBERON:0006238!1.26e-23!69;UBERON:0003080!3.66e-22!42;UBERON:0000025!6.93e-22!194;UBERON:0000477!2.11e-21!286;UBERON:0002780!2.39e-21!41;UBERON:0001890!2.39e-21!41;UBERON:0006240!2.39e-21!41;UBERON:0000119!5.32e-19!312;UBERON:0000483!7.59e-19!309;UBERON:0002020!1.08e-18!34;UBERON:0003528!1.08e-18!34;UBERON:0001893!2.33e-18!34;UBERON:0002791!8.24e-18!33;UBERON:0001869!4.82e-17!32;UBERON:0003056!2.33e-16!61;UBERON:0000153!1.39e-14!129;UBERON:0007811!1.39e-14!129;UBERON:0002619!4.88e-14!22;UBERON:0000033!7.40e-14!123;UBERON:0001986!8.47e-14!18;UBERON:0004638!8.47e-14!18;UBERON:0004852!8.47e-14!18;UBERON:0000956!6.44e-13!25;UBERON:0000203!6.44e-13!25;UBERON:0001950!8.65e-13!20;UBERON:0000924!2.20e-12!173;UBERON:0006601!2.20e-12!173;UBERON:0004121!2.75e-12!169;UBERON:0000487!1.53e-10!22;UBERON:0001009!1.61e-10!113;UBERON:0000468!2.28e-10!659;UBERON:0000467!5.08e-10!625;UBERON:0000480!6.98e-10!626;UBERON:0006914!1.03e-09!25;UBERON:0004535!2.17e-09!110;UBERON:0003076!3.46e-09!15;UBERON:0003057!3.46e-09!15;UBERON:0000922!1.13e-08!612;UBERON:0004732!3.02e-08!13;UBERON:0000481!4.08e-08!347;UBERON:0004733!1.84e-07!12;UBERON:0002028!1.84e-07!12;UBERON:0007277!1.84e-07!12;UBERON:0002050!1.87e-07!605;UBERON:0005423!1.87e-07!605;UBERON:0002308!2.19e-07!9;UBERON:0000125!2.19e-07!9;UBERON:0002298!2.89e-07!8;UBERON:0000923!3.33e-07!604;UBERON:0005291!3.33e-07!604;UBERON:0006598!3.33e-07!604;UBERON:0002532!3.33e-07!604;UBERON:0002420!3.95e-07!9;UBERON:0007245!3.95e-07!9;UBERON:0010009!3.95e-07!9;UBERON:0010011!3.95e-07!9;UBERON:0000454!3.95e-07!9;UBERON:0000064!4.28e-07!219;UBERON:0003915!6.42e-07!9;UBERON:0004700!6.42e-07!9;UBERON:0001917!6.42e-07!9
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}}
}}

Revision as of 19:43, 8 August 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 organism1.66e-61115
neural tube2.96e-3057
neural rod2.96e-3057
future spinal cord2.96e-3057
neural keel2.96e-3057
regional part of brain2.47e-2759
central nervous system1.86e-2682
neural plate3.41e-2486
presumptive neural plate3.41e-2486
anatomical conduit3.59e-24241
regional part of nervous system7.18e-2494
nervous system7.18e-2494
neurectoderm7.59e-2490
brain1.26e-2369
future brain1.26e-2369
anterior neural tube3.66e-2242
tube6.93e-22194
anatomical cluster2.11e-21286
regional part of forebrain2.39e-2141
forebrain2.39e-2141
future forebrain2.39e-2141
cell layer5.32e-19312
epithelium7.59e-19309
gray matter1.08e-1834
brain grey matter1.08e-1834
telencephalon2.33e-1834
regional part of telencephalon8.24e-1833
cerebral hemisphere4.82e-1732
pre-chordal neural plate2.33e-1661
anterior region of body1.39e-14129
craniocervical region1.39e-14129
regional part of cerebral cortex4.88e-1422
head7.40e-14123
endothelium8.47e-1418
blood vessel endothelium8.47e-1418
cardiovascular system endothelium8.47e-1418
cerebral cortex6.44e-1325
pallium6.44e-1325
neocortex8.65e-1320
ectoderm2.20e-12173
presumptive ectoderm2.20e-12173
ectoderm-derived structure2.75e-12169
simple squamous epithelium1.53e-1022
circulatory system1.61e-10113
multi-cellular organism2.28e-10659
anatomical system5.08e-10625
anatomical group6.98e-10626
squamous epithelium1.03e-0925
cardiovascular system2.17e-09110
posterior neural tube3.46e-0915
chordal neural plate3.46e-0915
embryo1.13e-08612
segmental subdivision of nervous system3.02e-0813
multi-tissue structure4.08e-08347
segmental subdivision of hindbrain1.84e-0712
hindbrain1.84e-0712
presumptive hindbrain1.84e-0712
embryonic structure1.87e-07605
developing anatomical structure1.87e-07605
nucleus of brain2.19e-079
neural nucleus2.19e-079
brainstem2.89e-078
germ layer3.33e-07604
embryonic tissue3.33e-07604
presumptive structure3.33e-07604
epiblast (generic)3.33e-07604
basal ganglion3.95e-079
nuclear complex of neuraxis3.95e-079
aggregate regional part of brain3.95e-079
collection of basal ganglia3.95e-079
cerebral subcortex3.95e-079
organ part4.28e-07219
endothelial tube6.42e-079
arterial system endothelium6.42e-079
endothelium of artery6.42e-079


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.