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Coexpression cluster:C4469: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.19e-38!115;UBERON:0001986!4.14e-17!18;UBERON:0004638!4.14e-17!18;UBERON:0004852!4.14e-17!18;UBERON:0004111!3.06e-16!241;UBERON:0000025!1.84e-15!194;UBERON:0000487!1.88e-13!22;UBERON:0001049!2.35e-13!57;UBERON:0005068!2.35e-13!57;UBERON:0006241!2.35e-13!57;UBERON:0007135!2.35e-13!57;UBERON:0000477!2.51e-13!286;UBERON:0003080!5.76e-13!42;UBERON:0002780!2.80e-12!41;UBERON:0001890!2.80e-12!41;UBERON:0006240!2.80e-12!41;UBERON:0006914!7.17e-12!25;UBERON:0002616!2.67e-11!59;UBERON:0000955!6.66e-11!69;UBERON:0006238!6.66e-11!69;UBERON:0001893!1.58e-10!34;UBERON:0001017!2.29e-10!82;UBERON:0002020!2.64e-10!34;UBERON:0003528!2.64e-10!34;UBERON:0002791!4.37e-10!33;UBERON:0005743!6.50e-10!86;UBERON:0001869!9.36e-10!32;UBERON:0003915!1.15e-09!9;UBERON:0004700!1.15e-09!9;UBERON:0001917!1.15e-09!9;UBERON:0000468!1.89e-09!659;UBERON:0000467!2.18e-09!625;UBERON:0000480!2.87e-09!626;UBERON:0000055!4.89e-09!69;UBERON:0000073!5.36e-09!94;UBERON:0001016!5.36e-09!94;UBERON:0002346!6.71e-09!90;UBERON:0003075!9.24e-09!86;UBERON:0007284!9.24e-09!86;UBERON:0004872!1.22e-08!84;UBERON:0002619!3.42e-08!22;UBERON:0000922!8.30e-08!612;UBERON:0001009!9.81e-08!113;UBERON:0001950!1.95e-07!20;UBERON:0002050!3.25e-07!605;UBERON:0005423!3.25e-07!605;UBERON:0000956!3.34e-07!25;UBERON:0000203!3.34e-07!25;UBERON:0003056!3.89e-07!61;UBERON:0000923!6.11e-07!604;UBERON:0005291!6.11e-07!604;UBERON:0006598!6.11e-07!604;UBERON:0002532!6.11e-07!604;UBERON:0000483!6.94e-07!309
|ontology_enrichment_uberon=UBERON:0007023!3.19e-38!115;UBERON:0001986!4.14e-17!18;UBERON:0004638!4.14e-17!18;UBERON:0004852!4.14e-17!18;UBERON:0004111!3.06e-16!241;UBERON:0000025!1.84e-15!194;UBERON:0000487!1.88e-13!22;UBERON:0001049!2.35e-13!57;UBERON:0005068!2.35e-13!57;UBERON:0006241!2.35e-13!57;UBERON:0007135!2.35e-13!57;UBERON:0000477!2.51e-13!286;UBERON:0003080!5.76e-13!42;UBERON:0002780!2.80e-12!41;UBERON:0001890!2.80e-12!41;UBERON:0006240!2.80e-12!41;UBERON:0006914!7.17e-12!25;UBERON:0002616!2.67e-11!59;UBERON:0000955!6.66e-11!69;UBERON:0006238!6.66e-11!69;UBERON:0001893!1.58e-10!34;UBERON:0001017!2.29e-10!82;UBERON:0002020!2.64e-10!34;UBERON:0003528!2.64e-10!34;UBERON:0002791!4.37e-10!33;UBERON:0005743!6.50e-10!86;UBERON:0001869!9.36e-10!32;UBERON:0003915!1.15e-09!9;UBERON:0004700!1.15e-09!9;UBERON:0001917!1.15e-09!9;UBERON:0000468!1.89e-09!659;UBERON:0000467!2.18e-09!625;UBERON:0000480!2.87e-09!626;UBERON:0000055!4.89e-09!69;UBERON:0000073!5.36e-09!94;UBERON:0001016!5.36e-09!94;UBERON:0002346!6.71e-09!90;UBERON:0003075!9.24e-09!86;UBERON:0007284!9.24e-09!86;UBERON:0004872!1.22e-08!84;UBERON:0002619!3.42e-08!22;UBERON:0000922!8.30e-08!612;UBERON:0001009!9.81e-08!113;UBERON:0001950!1.95e-07!20;UBERON:0002050!3.25e-07!605;UBERON:0005423!3.25e-07!605;UBERON:0000956!3.34e-07!25;UBERON:0000203!3.34e-07!25;UBERON:0003056!3.89e-07!61;UBERON:0000923!6.11e-07!604;UBERON:0005291!6.11e-07!604;UBERON:0006598!6.11e-07!604;UBERON:0002532!6.11e-07!604;UBERON:0000483!6.94e-07!309
|tf_chipseq_enrich=REST#5978;3:9.65002871612802:0.00111263624711459:0.00770267910727831
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}}
}}

Revision as of 13:25, 5 September 2012


Full id: C4469_Endothelial_lung_spleen_placenta_Hepatic_adipose_skeletal



Phase1 CAGE Peaks

Hg19::chr5:141337686..141337697,-p2@PCDH12
Hg19::chr5:141337703..141337712,-p4@PCDH12
Hg19::chr5:141337739..141337772,-p1@PCDH12


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 organism3.19e-38115
endothelium4.14e-1718
blood vessel endothelium4.14e-1718
cardiovascular system endothelium4.14e-1718
anatomical conduit3.06e-16241
tube1.84e-15194
simple squamous epithelium1.88e-1322
neural tube2.35e-1357
neural rod2.35e-1357
future spinal cord2.35e-1357
neural keel2.35e-1357
anatomical cluster2.51e-13286
anterior neural tube5.76e-1342
regional part of forebrain2.80e-1241
forebrain2.80e-1241
future forebrain2.80e-1241
squamous epithelium7.17e-1225
regional part of brain2.67e-1159
brain6.66e-1169
future brain6.66e-1169
telencephalon1.58e-1034
central nervous system2.29e-1082
gray matter2.64e-1034
brain grey matter2.64e-1034
regional part of telencephalon4.37e-1033
cerebral hemisphere9.36e-1032
endothelial tube1.15e-099
arterial system endothelium1.15e-099
endothelium of artery1.15e-099
multi-cellular organism1.89e-09659
anatomical system2.18e-09625
anatomical group2.87e-09626
vessel4.89e-0969
regional part of nervous system5.36e-0994
nervous system5.36e-0994
neurectoderm6.71e-0990
neural plate9.24e-0986
presumptive neural plate9.24e-0986
splanchnic layer of lateral plate mesoderm1.22e-0884
regional part of cerebral cortex3.42e-0822
embryo8.30e-08612
circulatory system9.81e-08113
neocortex1.95e-0720
embryonic structure3.25e-07605
developing anatomical structure3.25e-07605
cerebral cortex3.34e-0725
pallium3.34e-0725
pre-chordal neural plate3.89e-0761
germ layer6.11e-07604
embryonic tissue6.11e-07604
presumptive structure6.11e-07604
epiblast (generic)6.11e-07604
epithelium6.94e-07309


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
REST#597839.650028716128020.001112636247114590.00770267910727831



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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