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Coexpression cluster:C3059

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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 cell1.23e-25108
common myeloid progenitor1.23e-25108
hematopoietic stem cell1.52e-20168
angioblastic mesenchymal cell1.52e-20168
hematopoietic oligopotent progenitor cell7.29e-19161
hematopoietic multipotent progenitor cell7.29e-19161
hematopoietic cell1.10e-18177
endothelial cell2.12e-1536
myeloid leukocyte1.96e-1472
endothelial cell of vascular tree1.31e-1224
granulocyte monocyte progenitor cell2.22e-1267
meso-epithelial cell8.30e-1245
myeloid lineage restricted progenitor cell5.15e-1166
macrophage dendritic cell progenitor8.24e-1161
monopoietic cell2.01e-1059
monocyte2.01e-1059
monoblast2.01e-1059
promonocyte2.01e-1059
blood vessel endothelial cell3.44e-1018
embryonic blood vessel endothelial progenitor cell3.44e-1018
leukocyte4.65e-10136
defensive cell8.35e-0948
phagocyte8.35e-0948
B cell9.23e-0914
hematopoietic lineage restricted progenitor cell3.02e-07120
classical monocyte3.26e-0742
CD14-positive, CD16-negative classical monocyte3.26e-0742
nongranular leukocyte3.57e-07115
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.15e-21203
epithelial tube1.01e-15117
cardiovascular system1.48e-15109
vessel1.52e-1568
circulatory system1.54e-15112
epithelial tube open at both ends3.49e-1459
blood vessel3.49e-1459
blood vasculature3.49e-1459
vascular cord3.49e-1459
hemolymphoid system1.75e-13108
vasculature1.88e-1378
vascular system1.88e-1378
splanchnic layer of lateral plate mesoderm1.62e-1283
immune system2.52e-1193
hematopoietic system6.37e-1198
blood island6.37e-1198
blood vessel endothelium3.44e-1018
endothelium3.44e-1018
cardiovascular system endothelium3.44e-1018
bone marrow1.53e-0976
bone element3.04e-0982
tube4.20e-09192
artery4.50e-0942
arterial blood vessel4.50e-0942
arterial system4.50e-0942
simple squamous epithelium7.63e-0922
mesoderm1.32e-08315
mesoderm-derived structure1.32e-08315
presumptive mesoderm1.32e-08315
anatomical conduit5.34e-08240
systemic artery9.08e-0733
systemic arterial system9.08e-0733
Disease
Ontology termp-valuen
myeloid leukemia5.83e-1531
leukemia1.03e-1039
hematologic cancer1.16e-0751
immune system cancer1.16e-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.