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Coexpression cluster:C3059: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3059_thyroid_Renal_Smooth_Hepatic_acute_CD34_Endothelial
|full_id=C3059_thyroid_Renal_Smooth_Hepatic_acute_CD34_Endothelial
|id=C3059
|id=C3059

Revision as of 15:54, 12 September 2012


Full id: C3059_thyroid_Renal_Smooth_Hepatic_acute_CD34_Endothelial



Phase1 CAGE Peaks

Hg19::chr10:94449649..94449664,+p3@HHEX
Hg19::chr10:94449675..94449694,+p2@HHEX
Hg19::chr10:94449703..94449718,+p1@HHEX


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>disease_data<br>

Cell Type
Ontology termp-valuen
myeloid cell1.73e-28112
common myeloid progenitor1.73e-28112
hematopoietic stem cell1.65e-22172
angioblastic mesenchymal cell1.65e-22172
hematopoietic cell2.86e-21182
hematopoietic oligopotent progenitor cell7.68e-21165
hematopoietic multipotent progenitor cell7.68e-21165
myeloid leukocyte5.33e-1776
endothelial cell8.76e-1635
granulocyte monocyte progenitor cell3.27e-1571
myeloid lineage restricted progenitor cell1.27e-1370
macrophage dendritic cell progenitor1.92e-1365
monopoietic cell5.86e-1363
monocyte5.86e-1363
monoblast5.86e-1363
promonocyte5.86e-1363
endothelial cell of vascular tree8.21e-1324
meso-epithelial cell1.03e-1144
leukocyte1.03e-11140
blood vessel endothelial cell5.06e-1018
embryonic blood vessel endothelial progenitor cell5.06e-1018
classical monocyte8.68e-1045
CD14-positive, CD16-negative classical monocyte3.33e-0942
hematopoietic lineage restricted progenitor cell7.54e-09124
nongranular leukocyte1.18e-08119
B cell1.47e-0814
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.97e-23216
cardiovascular system8.16e-18110
circulatory system1.04e-17113
epithelial tube4.06e-17118
vessel7.69e-1769
immune system1.66e-16115
hemolymphoid system5.11e-16112
vasculature1.98e-1579
vascular system1.98e-1579
blood vessel2.64e-1560
epithelial tube open at both ends2.64e-1560
blood vasculature2.64e-1560
vascular cord2.64e-1560
splanchnic layer of lateral plate mesoderm2.47e-1384
hematopoietic system3.13e-13102
blood island3.13e-13102
bone marrow1.20e-1180
bone element2.74e-1186
artery1.47e-1042
arterial blood vessel1.47e-1042
arterial system1.47e-1042
endothelium5.06e-1018
blood vessel endothelium5.06e-1018
cardiovascular system endothelium5.06e-1018
tube1.17e-09194
unilaminar epithelium2.15e-09138
simple squamous epithelium9.66e-0922
anatomical conduit2.03e-08241
systemic artery5.30e-0833
systemic arterial system5.30e-0833
mesoderm6.75e-08448
mesoderm-derived structure6.75e-08448
presumptive mesoderm6.75e-08448
anatomical cluster1.08e-07286
Disease
Ontology termp-valuen
myeloid leukemia1.43e-1431
leukemia3.24e-1039
hematologic cancer5.13e-0751
immune system cancer5.13e-0751


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
CCNT2#90536.336201576962630.003930750035764890.0189094243659719
E2F1#186934.907389214879320.008460985347239390.0323506076763805
E2F4#1874312.66806031528440.0004917987006298980.00435279360127847
E2F6#187635.017155731697390.00791769806886330.0320324024254896
EGR1#195834.988179094810140.008056488137383440.0319006507650966
ELF1#199734.258097958807540.01295179875054610.0459983306596485
GABPB1#255337.067683836182170.002832212825417420.0153627025695321
HMGN3#932438.178547723350590.001827766942164210.0108281894419813
SIN3A#2594235.408884726815140.006318961977991520.027534465538195
SUZ12#23512350.11578091106297.93834897779404e-060.000221145166415533



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3059&oldid=2137806"