Coexpression cluster:C4591

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

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p.value	FDR	nGenes	nPathway	Name
5.08218999092061e-05	0.00268085522021062	2	204	Endocytosis (KEGG):04144
2.96743344876993e-05	0.00170762306642851	2	156	Phagosome (KEGG):04145
2.25318768070372e-05	0.00144739769524672	2	136	Cell adhesion molecules (CAMs) (KEGG):04514
7.37072179210596e-06	0.000583208361800384	2	78	Antigen processing and presentation (KEGG):04612
2.28656823893637e-05	0.00144739769524672	2	137	Natural killer cell mediated cytotoxicity (KEGG):04650
2.42990828311186e-06	0.00044465996176429	2	45	Type I diabetes mellitus (KEGG):04940
3.51232197286169e-06	0.00044465996176429	2	54	Autoimmune thyroid disease (KEGG):05320
1.81874953311705e-06	0.00044465996176429	2	39	Allograft rejection (KEGG):05330
2.21637088853536e-06	0.00044465996176429	2	43	Graft-versus-host disease (KEGG):05332
6.2735813854888e-06	0.00056731100243063	2	72	Viral myocarditis (KEGG):05416
4.94817686742777e-06	0.00052203265951363	2	64	Proteasome Degradation (Wikipathways):WP183
0.000319827473566556	0.0155731377513561	2	511	Signaling in Immune system (Reactome):REACT_6900
3.12942733431072e-06	0.00044465996176429	2	51	{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

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GO ID	GO name	FDR corrected p-value
GO:0032393	MHC class I receptor activity	0.0216649005062993
GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	0.0236959849287649
GO:0048002	antigen processing and presentation of peptide antigen	0.0236959849287649
GO:0042612	MHC class I protein complex	0.039098375132462
GO:0042611	MHC protein complex	0.0468277797401782
GO:0019882	antigen processing and presentation	0.0468277797401782

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>

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Cell Type

Ontology term	p-value	n
leukocyte	2.17e-31	136
myeloid leukocyte	7.60e-27	72
nongranular leukocyte	2.04e-26	115
defensive cell	2.88e-25	48
phagocyte	2.88e-25	48
hematopoietic lineage restricted progenitor cell	1.21e-24	120
macrophage dendritic cell progenitor	6.84e-24	61
classical monocyte	1.10e-23	42
CD14-positive, CD16-negative classical monocyte	1.10e-23	42
monopoietic cell	2.86e-23	59
monocyte	2.86e-23	59
monoblast	2.86e-23	59
promonocyte	2.86e-23	59
granulocyte monocyte progenitor cell	5.72e-23	67
myeloid lineage restricted progenitor cell	7.68e-21	66
hematopoietic stem cell	1.33e-18	168
angioblastic mesenchymal cell	1.33e-18	168
hematopoietic oligopotent progenitor cell	2.46e-18	161
hematopoietic multipotent progenitor cell	2.46e-18	161
hematopoietic cell	6.46e-18	177
myeloid cell	1.67e-13	108
common myeloid progenitor	1.67e-13	108
stuff accumulating cell	8.99e-11	87
mesenchymal cell	3.43e-08	354
multi fate stem cell	3.26e-07	427
connective tissue cell	3.26e-07	361

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.33e-26	108
hematopoietic system	2.62e-25	98
blood island	2.62e-25	98
immune system	4.98e-22	93
bone marrow	5.87e-19	76
bone element	9.88e-18	82
lateral plate mesoderm	1.71e-15	203
skeletal element	1.74e-13	90
skeletal system	4.21e-11	100
mesoderm	7.16e-09	315
mesoderm-derived structure	7.16e-09	315
presumptive mesoderm	7.16e-09	315
musculoskeletal system	5.03e-07	167
connective tissue	6.73e-07	371

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

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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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
IRF4#3662	2	14.6096751244961	0.00605612247321789	0.0268575530777241
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270713594757579
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324967560010806
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381596102465473
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00486517933878103

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

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This analysis result is provided for C0 - C305 clusters.