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Coexpression cluster:C4512

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Full id: C4512_CD4_Neutrophils_CD14_plasma_CD8_Peripheral_Eosinophils



Phase1 CAGE Peaks

Hg19::chr5:64859206..64859218,+p3@PPWD1
Hg19::chr5:64859227..64859241,+p2@PPWD1
Hg19::chrX:11778228..11778347,+p2@MSL3


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


GO IDGO nameFDR corrected p-value
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.0406216884493112
GO:0016859cis-trans isomerase activity0.0406216884493112
GO:0005681spliceosome0.0406216884493112
GO:0008380RNA splicing0.0406216884493112
GO:0006397mRNA processing0.0406216884493112
GO:0016853isomerase activity0.0406216884493112
GO:0016071mRNA metabolic process0.0406216884493112
GO:0006457protein folding0.0406216884493112



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
leukocyte4.81e-47136
hematopoietic stem cell1.08e-46168
angioblastic mesenchymal cell1.08e-46168
hematopoietic cell2.73e-44177
hematopoietic oligopotent progenitor cell7.56e-43161
hematopoietic multipotent progenitor cell7.56e-43161
nongranular leukocyte1.96e-38115
hematopoietic lineage restricted progenitor cell1.71e-36120
myeloid cell8.76e-23108
common myeloid progenitor8.76e-23108
myeloid leukocyte1.01e-2172
classical monocyte1.08e-2142
CD14-positive, CD16-negative classical monocyte1.08e-2142
granulocyte monocyte progenitor cell6.79e-1967
lymphocyte8.52e-1953
common lymphoid progenitor8.52e-1953
macrophage dendritic cell progenitor1.48e-1861
lymphoid lineage restricted progenitor cell2.68e-1852
nucleate cell7.21e-1855
defensive cell1.31e-1748
phagocyte1.31e-1748
monopoietic cell1.32e-1759
monocyte1.32e-1759
monoblast1.32e-1759
promonocyte1.32e-1759
myeloid lineage restricted progenitor cell6.92e-1766
mature alpha-beta T cell2.53e-1118
alpha-beta T cell2.53e-1118
immature T cell2.53e-1118
mature T cell2.53e-1118
immature alpha-beta T cell2.53e-1118
mesenchymal cell1.28e-10354
T cell4.14e-1025
pro-T cell4.14e-1025
motile cell1.04e-09386
connective tissue cell2.79e-09361
B cell3.91e-0814
lymphocyte of B lineage5.76e-0824
pro-B cell5.76e-0824
CD8-positive, alpha-beta T cell1.04e-0711
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.13e-24108
hematopoietic system3.93e-2398
blood island3.93e-2398
immune system4.08e-1993
bone marrow3.34e-1576
bone element1.61e-1482
skeletal element3.36e-1290
skeletal system8.16e-10100
connective tissue3.34e-09371
lateral plate mesoderm6.45e-07203
blood8.22e-0715
haemolymphatic fluid8.22e-0715
organism substance8.22e-0715


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
ATF3#467214.97544968400580.005768294540793880.0259692608649871
BRCA1#672213.45615376214920.007119807716084560.0296426389499763
IRF3#3661231.32130147432640.001339514673320110.00887900310782429
MAFK#7975218.06715542521990.003983674744936810.0191173554512914
NFYA#4800212.28372046655370.008516011403724430.0324908203037033
NFYB#4801211.17319550235760.01025467135054530.0381514541600028
NR3C1#290829.982015554115360.01278474365547170.046074045639538
SIX5#147912211.3911435703060.009873820081429030.0370886165833825



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.