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Coexpression cluster:C4591

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Full id: C4591_Neutrophils_Basophils_Eosinophils_migratory_CD14_CD4_CD8



Phase1 CAGE Peaks

Hg19::chr6:31239114..31239134,-p6@HLA-C
Hg19::chr6:31239852..31239876,-p1@HLA-C
Hg19::chr6:31324943..31324963,-p1@HLA-B


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


p.valueFDRnGenesnPathwayName
5.08218999092061e-050.002680855220210622204Endocytosis (KEGG):04144
2.96743344876993e-050.001707623066428512156Phagosome (KEGG):04145
2.25318768070372e-050.001447397695246722136Cell adhesion molecules (CAMs) (KEGG):04514
7.37072179210596e-060.000583208361800384278Antigen processing and presentation (KEGG):04612
2.28656823893637e-050.001447397695246722137Natural killer cell mediated cytotoxicity (KEGG):04650
2.42990828311186e-060.00044465996176429245Type I diabetes mellitus (KEGG):04940
3.51232197286169e-060.00044465996176429254Autoimmune thyroid disease (KEGG):05320
1.81874953311705e-060.00044465996176429239Allograft rejection (KEGG):05330
2.21637088853536e-060.00044465996176429243Graft-versus-host disease (KEGG):05332
6.2735813854888e-060.00056731100243063272Viral myocarditis (KEGG):05416
4.94817686742777e-060.00052203265951363264Proteasome Degradation (Wikipathways):WP183
0.0003198274735665560.01557313775135612511Signaling in Immune system (Reactome):REACT_6900
3.12942733431072e-060.00044465996176429251{HLA-A,53} (Static Module):NA



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:0032393MHC class I receptor activity0.0216649005062993
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0236959849287649
GO:0048002antigen processing and presentation of peptide antigen0.0236959849287649
GO:0042612MHC class I protein complex0.039098375132462
GO:0042611MHC protein complex0.0468277797401782
GO:0019882antigen processing and presentation0.0468277797401782



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
leukocyte9.75e-37140
nongranular leukocyte2.22e-31119
hematopoietic lineage restricted progenitor cell4.20e-29124
myeloid leukocyte6.70e-2676
CD14-positive, CD16-negative classical monocyte1.09e-2442
macrophage dendritic cell progenitor1.10e-2265
hematopoietic stem cell3.62e-22172
angioblastic mesenchymal cell3.62e-22172
monopoietic cell4.03e-2263
monocyte4.03e-2263
monoblast4.03e-2263
promonocyte4.03e-2263
granulocyte monocyte progenitor cell5.69e-2271
hematopoietic cell1.47e-21182
hematopoietic oligopotent progenitor cell1.85e-21165
hematopoietic multipotent progenitor cell1.85e-21165
classical monocyte1.86e-2045
myeloid lineage restricted progenitor cell3.94e-2070
myeloid cell1.12e-12112
common myeloid progenitor1.12e-12112
mesenchymal cell1.48e-09358
lymphoid lineage restricted progenitor cell7.32e-0952
lymphocyte7.40e-0953
common lymphoid progenitor7.40e-0953
multi fate stem cell1.32e-08430
connective tissue cell1.51e-08365
somatic stem cell2.11e-07436
stem cell2.50e-07444
mature alpha-beta T cell7.21e-0718
alpha-beta T cell7.21e-0718
immature T cell7.21e-0718
mature T cell7.21e-0718
immature alpha-beta T cell7.21e-0718
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.74e-28112
hematopoietic system1.07e-26102
blood island1.07e-26102
bone marrow6.32e-1980
immune system1.03e-17115
bone element3.36e-1786
lateral plate mesoderm5.49e-16216
skeletal element6.69e-12101
skeletal system6.69e-12101
connective tissue2.09e-08375
musculoskeletal system8.89e-08167
blood7.19e-0715
haemolymphatic fluid7.19e-0715
organism substance7.19e-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
IRF4#3662214.60967512449610.006056122473217890.0268575530777241
NFKB1#479035.488063424193840.006049381815655430.0270713594757579
NFYA#4800212.28372046655370.008516011403724430.0324967560010806
NFYB#4801211.17319550235760.01025467135054530.0381596102465473
RFX5#5993312.04791082719510.0005717246050312580.00486517933878103



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.