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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3289_lung_Endothelial_Renal_Hepatic_Lymphatic_adipose_breast
|full_id=C3289_lung_Endothelial_Renal_Hepatic_Lymphatic_adipose_breast
|id=C3289
|id=C3289

Revision as of 16:11, 12 September 2012


Full id: C3289_lung_Endothelial_Renal_Hepatic_Lymphatic_adipose_breast



Phase1 CAGE Peaks

Hg19::chr12:52306161..52306194,+p3@ACVRL1
Hg19::chr12:52306196..52306215,+p6@ACVRL1
Hg19::chr12:52306220..52306231,+p9@ACVRL1


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 organism1.56e-39115
anatomical conduit1.76e-20241
tube1.65e-19194
anatomical cluster1.68e-19286
neural tube6.36e-1957
neural rod6.36e-1957
future spinal cord6.36e-1957
neural keel6.36e-1957
brain1.91e-1669
future brain1.91e-1669
regional part of brain1.96e-1659
central nervous system4.45e-1682
endothelium7.65e-1618
blood vessel endothelium7.65e-1618
cardiovascular system endothelium7.65e-1618
anterior neural tube1.10e-1442
regional part of forebrain5.00e-1441
forebrain5.00e-1441
future forebrain5.00e-1441
regional part of nervous system2.61e-1394
nervous system2.61e-1394
neural plate4.50e-1386
presumptive neural plate4.50e-1386
gray matter8.70e-1334
brain grey matter8.70e-1334
multi-cellular organism1.64e-12659
telencephalon2.37e-1234
anatomical system2.65e-12625
anatomical group3.80e-12626
simple squamous epithelium4.02e-1222
neurectoderm5.83e-1290
vessel6.52e-1269
regional part of telencephalon6.61e-1233
cerebral hemisphere1.79e-1132
squamous epithelium2.50e-1125
vasculature1.04e-1079
vascular system1.04e-1079
regional part of cerebral cortex1.86e-1022
cell layer6.47e-10312
epithelium1.27e-09309
embryo1.88e-09612
neocortex2.95e-0920
circulatory system4.96e-09113
splanchnic layer of lateral plate mesoderm7.10e-0984
anterior region of body9.56e-09129
craniocervical region9.56e-09129
embryonic structure9.88e-09605
developing anatomical structure9.88e-09605
endothelial tube1.07e-089
arterial system endothelium1.07e-089
endothelium of artery1.07e-089
germ layer1.98e-08604
embryonic tissue1.98e-08604
presumptive structure1.98e-08604
epiblast (generic)1.98e-08604
blood vessel2.07e-0860
epithelial tube open at both ends2.07e-0860
blood vasculature2.07e-0860
vascular cord2.07e-0860
cerebral cortex2.89e-0825
pallium2.89e-0825
pre-chordal neural plate3.09e-0861
head3.99e-08123
cardiovascular system4.11e-08110
lymphoid system5.21e-0810
epithelial tube3.77e-07118
organ4.06e-07511
lymphatic vessel5.04e-078
lymph vasculature5.04e-078
lymphatic part of lymphoid system5.04e-078
brainstem6.94e-078


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
GATA2#2624312.7449317335540.0004829527704283790.00436211228840003
SPI1#668838.204323508522730.001810593189410520.0108888945127747
ZNF263#1012738.221841637010680.001799043925565870.0109029390438214



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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