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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:59, 8 August 2012


Full id: C3200_Endothelial_Hepatic_Lymphatic_testicular_Renal_lung_Mast



Phase1 CAGE Peaks

Hg19::chr11:75062661..75062685,-p4@ARRB1
Hg19::chr11:75062686..75062723,-p1@ARRB1
Hg19::chr11:75062730..75062775,-p3@ARRB1


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
myeloid cell1.74e-25112
common myeloid progenitor1.74e-25112
myeloid leukocyte5.30e-2276
granulocyte monocyte progenitor cell5.79e-2171
myeloid lineage restricted progenitor cell5.96e-1970
endothelial cell9.88e-1935
macrophage dendritic cell progenitor2.79e-1865
monopoietic cell3.84e-1863
monocyte3.84e-1863
monoblast3.84e-1863
promonocyte3.84e-1863
CD14-positive, CD16-negative classical monocyte4.33e-1642
meso-epithelial cell1.15e-1444
endothelial cell of vascular tree1.36e-1424
classical monocyte2.26e-1445
blood vessel endothelial cell3.72e-1118
embryonic blood vessel endothelial progenitor cell3.72e-1118
lining cell5.29e-0957
barrier cell5.29e-0957
hematopoietic oligopotent progenitor cell6.51e-08165
hematopoietic multipotent progenitor cell6.51e-08165
hematopoietic stem cell1.29e-07172
angioblastic mesenchymal cell1.29e-07172
hematopoietic cell3.48e-07182
Uber Anatomy
Ontology termp-valuen
hemolymphoid system8.58e-23112
adult organism3.98e-22115
hematopoietic system3.21e-19102
blood island3.21e-19102
immune system1.31e-18115
bone marrow1.88e-1680
bone element1.81e-1386
endothelium3.72e-1118
blood vessel endothelium3.72e-1118
cardiovascular system endothelium3.72e-1118
lateral plate mesoderm5.70e-11216
telencephalon2.54e-1034
neural tube2.90e-1057
neural rod2.90e-1057
future spinal cord2.90e-1057
neural keel2.90e-1057
gray matter3.64e-1034
brain grey matter3.64e-1034
regional part of telencephalon7.71e-1033
regional part of cerebral cortex7.88e-1022
cerebral hemisphere1.03e-0932
anterior neural tube1.83e-0942
regional part of brain2.08e-0959
neocortex3.49e-0920
regional part of forebrain3.52e-0941
forebrain3.52e-0941
future forebrain3.52e-0941
simple squamous epithelium4.74e-0922
skeletal element1.19e-08101
skeletal system1.19e-08101
central nervous system1.61e-0882
brain3.25e-0869
future brain3.25e-0869
squamous epithelium1.10e-0725
cerebral cortex6.27e-0725
pallium6.27e-0725
regional part of nervous system7.35e-0794
nervous system7.35e-0794


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.

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