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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3390_Endothelial_lung_corpus_optic_adipose_thalamus_globus
|full_id=C3390_Endothelial_lung_corpus_optic_adipose_thalamus_globus
|id=C3390
|id=C3390

Revision as of 16:18, 12 September 2012


Full id: C3390_Endothelial_lung_corpus_optic_adipose_thalamus_globus



Phase1 CAGE Peaks

Hg19::chr13:99630233..99630348,-p1@DOCK9
Hg19::chr8:17555164..17555204,-p1@MTUS1
Hg19::chr8:68864330..68864361,+p3@PREX2


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 organism3.53e-44115
anatomical conduit2.87e-29241
anatomical cluster3.06e-29286
neural tube1.99e-2657
neural rod1.99e-2657
future spinal cord1.99e-2657
neural keel1.99e-2657
cell layer5.89e-26312
regional part of brain9.35e-2659
tube1.86e-25194
central nervous system1.94e-2582
epithelium2.74e-25309
brain9.10e-2569
future brain9.10e-2569
regional part of nervous system3.76e-2494
nervous system3.76e-2494
neural plate2.28e-2286
presumptive neural plate2.28e-2286
anterior neural tube2.43e-2142
regional part of forebrain9.47e-2141
forebrain9.47e-2141
future forebrain9.47e-2141
neurectoderm1.20e-2090
anterior region of body7.43e-19129
craniocervical region7.43e-19129
head3.22e-18123
telencephalon1.58e-1734
gray matter1.63e-1734
brain grey matter1.63e-1734
regional part of telencephalon6.25e-1733
pre-chordal neural plate9.20e-1761
cerebral hemisphere3.39e-1632
ectoderm-derived structure4.40e-16169
multi-tissue structure2.12e-15347
ectoderm3.03e-15173
presumptive ectoderm3.03e-15173
regional part of cerebral cortex5.86e-1322
organism subdivision1.41e-12365
cerebral cortex5.35e-1225
pallium5.35e-1225
neocortex8.61e-1220
multi-cellular organism1.32e-11659
anatomical system1.41e-11625
anatomical group2.02e-11626
endothelium3.24e-1118
blood vessel endothelium3.24e-1118
cardiovascular system endothelium3.24e-1118
organ part4.55e-10219
embryo6.38e-10612
simple squamous epithelium1.55e-0922
embryonic structure1.75e-09605
developing anatomical structure1.75e-09605
circulatory system2.94e-09113
germ layer3.30e-09604
embryonic tissue3.30e-09604
presumptive structure3.30e-09604
epiblast (generic)3.30e-09604
squamous epithelium1.81e-0825
cardiovascular system2.06e-08110
compound organ2.25e-0869
vasculature6.12e-0879
vascular system6.12e-0879
splanchnic layer of lateral plate mesoderm2.25e-0784
nucleus of brain3.71e-079
neural nucleus3.71e-079
basal ganglion4.89e-079
nuclear complex of neuraxis4.89e-079
aggregate regional part of brain4.89e-079
collection of basal ganglia4.89e-079
cerebral subcortex4.89e-079
epithelial tube6.51e-07118


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.