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Coexpression cluster:C3347: Difference between revisions

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|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00895778349656121!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.032896021248661
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00895778349656121!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.032896021248661
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}}
}}

Revision as of 16:04, 26 November 2012


Full id: C3347_Endothelial_acute_Hepatic_Renal_Lymphatic_large_CD14



Phase1 CAGE Peaks

Hg19::chr12:96588368..96588394,+p3@ELK3
Hg19::chrX:71299606..71299619,+p@chrX:71299606..71299619
+
Hg19::chrX:71299620..71299649,+p@chrX:71299620..71299649
+


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>


Cell Type
Ontology termp-valuen
endothelial cell7.99e-2936
endothelial cell of vascular tree9.37e-2924
blood vessel endothelial cell4.45e-2218
embryonic blood vessel endothelial progenitor cell4.45e-2218
meso-epithelial cell1.85e-2045
classical monocyte1.49e-1442
CD14-positive, CD16-negative classical monocyte1.49e-1442
lining cell3.43e-1358
barrier cell3.43e-1358
defensive cell3.97e-1348
phagocyte3.97e-1348
endothelial cell of artery7.11e-129
myeloid leukocyte1.02e-0972
myeloid cell1.41e-09108
common myeloid progenitor1.41e-09108
myeloid lineage restricted progenitor cell2.18e-0966
monopoietic cell2.59e-0959
monocyte2.59e-0959
monoblast2.59e-0959
promonocyte2.59e-0959
granulocyte monocyte progenitor cell4.21e-0967
macrophage dendritic cell progenitor1.03e-0861
vein endothelial cell1.31e-086
aortic endothelial cell1.74e-086
lymphangioblast3.24e-086
endothelial cell of lymphatic vessel3.24e-086
vascular lymphangioblast3.24e-086
Uber Anatomy
Ontology termp-valuen
blood vessel endothelium4.45e-2218
endothelium4.45e-2218
cardiovascular system endothelium4.45e-2218
lateral plate mesoderm3.03e-18203
simple squamous epithelium1.07e-1622
adult organism2.50e-15114
vessel5.83e-1468
squamous epithelium7.90e-1425
vasculature1.18e-1278
vascular system1.18e-1278
circulatory system1.48e-12112
immune system3.44e-1293
mesoderm5.18e-12315
mesoderm-derived structure5.18e-12315
presumptive mesoderm5.18e-12315
endothelial tube7.11e-129
arterial system endothelium7.11e-129
endothelium of artery7.11e-129
splanchnic layer of lateral plate mesoderm2.07e-1183
cardiovascular system2.80e-11109
epithelial tube open at both ends9.47e-1159
blood vessel9.47e-1159
blood vasculature9.47e-1159
vascular cord9.47e-1159
hemolymphoid system2.78e-10108
epithelial tube6.64e-08117
bone marrow1.71e-0776
hematopoietic system6.23e-0798
blood island6.23e-0798
lymphoid system6.93e-0710
vein8.88e-079
venous blood vessel8.88e-079
venous system8.88e-079
anatomical conduit9.40e-07240


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
FOS#235338.99795530889440.001372499272417130.00895778349656121
TRIM28#10155212.39368336350830.008368344129438470.032896021248661



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.