Coexpression cluster:C1932

Full id: C1932_immature_migratory_Monocytederived_CD14_plasma_Dendritic_Macrophage

Phase1 CAGE Peaks

Hg19::chr4:10686355..10686365,-	p4@CLNK
Hg19::chr4:184181710..184181715,+	p@chr4:184181710..184181715 +
Hg19::chr6:32610954..32610967,+	p12@HLA-DQA1
Hg19::chr6:32709159..32709175,+	p1@HLA-DQA2
Hg19::chr6:32725594..32725620,-	p@chr6:32725594..32725620 -

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
8.87028067484744e-05	0.00350930479198652	2	156	Phagosome (KEGG):04145
6.73840783266509e-05	0.00292803571279427	2	136	Cell adhesion molecules (CAMs) (KEGG):04514
2.20729154564608e-05	0.00127019595308543	2	78	Antigen processing and presentation (KEGG):04612
8.64980401661253e-06	0.000896112020211999	2	49	Intestinal immune network for IgA production (KEGG):04672
7.28240379719336e-06	0.000896112020211999	2	45	Type I diabetes mellitus (KEGG):04940
1.9318817157557e-05	0.00122288112607336	2	73	Leishmaniasis (KEGG):05140
6.44378011191878e-05	0.00292803571279427	2	133	Toxoplasmosis (KEGG):05145
1.1325270397624e-05	0.000896112020211999	2	56	Staphylococcus aureus infection (KEGG):05150
0.000120772003400194	0.00424714878624014	2	182	Tuberculosis (KEGG):05152
0.000112934890859989	0.00420516387731604	2	176	Influenza A (KEGG):05164
3.42164256458367e-06	0.000896112020211999	2	31	Asthma (KEGG):05310
1.05241687813521e-05	0.000896112020211999	2	54	Autoimmune thyroid disease (KEGG):05320
6.93847325306698e-05	0.00292803571279427	2	138	Systemic lupus erythematosus (KEGG):05322
3.0758227865789e-05	0.00162249651992037	2	92	Rheumatoid arthritis (KEGG):05323
5.45153351157612e-06	0.000896112020211999	2	39	Allograft rejection (KEGG):05330
6.64274556874299e-06	0.000896112020211999	2	43	Graft-versus-host disease (KEGG):05332
1.87899740683929e-05	0.00122288112607336	2	72	Viral myocarditis (KEGG):05416
0.000948076017669582	0.0315859010097287	2	511	Signaling in Immune system (Reactome):REACT_6900
2.85609257642289e-06	0.000896112020211999	3	406	{GRB2,414} (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:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	0.000172425623571692
GO:0042613	MHC class II protein complex	0.000172425623571692
GO:0042611	MHC protein complex	0.000818807252234725
GO:0019882	antigen processing and presentation	0.000818807252234725
GO:0032395	MHC class II receptor activity	0.00448787011083415
GO:0006955	immune response	0.00448787011083415
GO:0002376	immune system process	0.00522767039823827
GO:0044459	plasma membrane part	0.0124361385279608
GO:0043234	protein complex	0.0175990547962191
GO:0005886	plasma membrane	0.026123025269096
GO:0032991	macromolecular complex	0.026123025269096

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	3.09e-40	136
macrophage dendritic cell progenitor	1.24e-38	61
nongranular leukocyte	1.33e-38	115
hematopoietic lineage restricted progenitor cell	5.10e-37	120
monopoietic cell	1.37e-34	59
monocyte	1.37e-34	59
monoblast	1.37e-34	59
promonocyte	1.37e-34	59
granulocyte monocyte progenitor cell	2.23e-34	67
defensive cell	9.54e-34	48
phagocyte	9.54e-34	48
classical monocyte	9.07e-31	42
CD14-positive, CD16-negative classical monocyte	9.07e-31	42
myeloid lineage restricted progenitor cell	4.84e-30	66
hematopoietic stem cell	5.36e-30	168
angioblastic mesenchymal cell	5.36e-30	168
hematopoietic cell	3.89e-29	177
hematopoietic oligopotent progenitor cell	5.03e-29	161
hematopoietic multipotent progenitor cell	5.03e-29	161
myeloid leukocyte	7.62e-27	72
myeloid cell	1.28e-22	108
common myeloid progenitor	1.28e-22	108
Langerhans cell	2.98e-15	5
stuff accumulating cell	3.23e-15	87
conventional dendritic cell	4.07e-15	8
dendritic cell	3.88e-12	10
lymphocyte of B lineage	2.51e-11	24
pro-B cell	2.51e-11	24
intermediate monocyte	2.79e-10	9
CD14-positive, CD16-positive monocyte	2.79e-10	9
immature conventional dendritic cell	8.71e-08	5
common dendritic progenitor	8.71e-08	5
mesenchymal cell	1.72e-07	354
CD1a-positive Langerhans cell	3.90e-07	2
immature CD1a-positive Langerhans cell	3.90e-07	2
connective tissue cell	4.06e-07	361
lymphoid lineage restricted progenitor cell	9.93e-07	52

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.55e-42	98
blood island	2.55e-42	98
hemolymphoid system	1.58e-41	108
immune system	6.62e-39	93
bone marrow	3.30e-31	76
bone element	2.98e-28	82
skeletal element	6.34e-25	90
skeletal system	1.61e-21	100
lateral plate mesoderm	2.07e-16	203
hemopoietic organ	3.53e-12	7
immune organ	3.53e-12	7
musculoskeletal system	3.70e-10	167
mesoderm	3.71e-08	315
mesoderm-derived structure	3.71e-08	315
presumptive mesoderm	3.71e-08	315
spleen	6.39e-08	3
gastrointestinal system mesentery	6.39e-08	3
stomach region	6.39e-08	3
mesentery	6.39e-08	3
gastrointestinal system serosa	6.39e-08	3
mesentery of stomach	6.39e-08	3
gut mesentery	6.39e-08	3
dorsal mesentery	6.39e-08	3
dorsal mesogastrium	6.39e-08	3
peritoneal cavity	6.39e-08	3
spleen primordium	6.39e-08	3

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)
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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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No analysis results for this cluster

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.