Coexpression cluster:C500

Full id: C500_Neutrophils_Monocytederived_blood_CD14_Eosinophils_lung_mixed

Phase1 CAGE Peaks

Hg19::chr12:65090856..65090873,+	p@chr12:65090856..65090873 +
Hg19::chr15:45007619..45007649,+	p6@B2M
Hg19::chr15:45007659..45007713,+	p3@B2M
Hg19::chr15:45007740..45007774,+	p5@B2M
Hg19::chr15:45007776..45007836,+	p2@B2M
Hg19::chr15:45009798..45009900,+	p@chr15:45009798..45009900 +
Hg19::chr15:45009902..45010022,+	p@chr15:45009902..45010022 +
Hg19::chr1:203276836..203276855,+	p@chr1:203276836..203276855 +
Hg19::chr6:29691484..29691495,+	p3@HLA-F
Hg19::chr6:30458007..30458044,+	p@chr6:30458007..30458044 +
Hg19::chr6:30458081..30458117,+	p@chr6:30458081..30458117 +
Hg19::chr6:30458196..30458253,+	p@chr6:30458196..30458253 +
Hg19::chr6:30460680..30460737,+	p@chr6:30460680..30460737 +
Hg19::chr6:31239406..31239455,+	p@chr6:31239406..31239455 +
Hg19::chr6:31321862..31321941,-	p1@X07061 p1@X07062
Hg19::chr6:31322867..31322902,+	p@chr6:31322867..31322902 +
Hg19::chr6:31322916..31322974,-	p4@HLA-B
Hg19::chr6:31323216..31323285,-	p3@HLA-C p5@HLA-B
Hg19::chr6:31324641..31324664,-	p10@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
0.000151746387523186	0.00800462194184805	2	204	Endocytosis (KEGG):04144
8.87028067484744e-05	0.00510444333379857	2	156	Phagosome (KEGG):04145
6.73840783266509e-05	0.004265412158077	2	136	Cell adhesion molecules (CAMs) (KEGG):04514
1.96249599285332e-08	6.21129981738076e-06	3	78	Antigen processing and presentation (KEGG):04612
7.28240379719336e-06	0.000768293600603899	2	45	Type I diabetes mellitus (KEGG):04940
1.05241687813521e-05	0.000951685548370838	2	54	Autoimmune thyroid disease (KEGG):05320
5.45153351157612e-06	0.000768293600603899	2	39	Allograft rejection (KEGG):05330
6.64274556874299e-06	0.000768293600603899	2	43	Graft-versus-host disease (KEGG):05332
1.87899740683929e-05	0.00132156150947697	2	72	Viral myocarditis (KEGG):05416
1.48230348787841e-05	0.00117287263478379	2	64	Proteasome Degradation (Wikipathways):WP183
5.70320151504265e-06	0.000768293600603899	3	511	Signaling in Immune system (Reactome):REACT_6900
5.37212511845661e-09	3.40055519998304e-06	3	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:0002474	antigen processing and presentation of peptide antigen via MHC class I	3.44283425591547e-07
GO:0048002	antigen processing and presentation of peptide antigen	3.44283425591547e-07
GO:0042612	MHC class I protein complex	2.48279173867282e-06
GO:0042611	MHC protein complex	7.44220434057843e-06
GO:0019882	antigen processing and presentation	8.68789839607204e-06
GO:0032393	MHC class I receptor activity	1.03087902489797e-05
GO:0006955	immune response	0.000146634857782203
GO:0002376	immune system process	0.000203303733848579
GO:0044459	plasma membrane part	0.000810460688395914
GO:0043234	protein complex	0.00146544028199587
GO:0005886	plasma membrane	0.0029844998842909
GO:0032991	macromolecular complex	0.0029844998842909
GO:0004888	transmembrane receptor activity	0.0188521394295296
GO:0044425	membrane part	0.0201582891042318
GO:0004872	receptor activity	0.0354197492238477
GO:0016020	membrane	0.0354197492238477
GO:0004871	signal transducer activity	0.0442459626345693
GO:0060089	molecular transducer activity	0.0442459626345693

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	2.94e-45	136
nongranular leukocyte	2.60e-40	115
hematopoietic lineage restricted progenitor cell	9.46e-36	120
hematopoietic stem cell	3.14e-31	168
angioblastic mesenchymal cell	3.14e-31	168
hematopoietic cell	4.59e-30	177
hematopoietic oligopotent progenitor cell	6.78e-30	161
hematopoietic multipotent progenitor cell	6.78e-30	161
defensive cell	1.44e-28	48
phagocyte	1.44e-28	48
myeloid leukocyte	1.98e-28	72
macrophage dendritic cell progenitor	5.28e-27	61
monopoietic cell	2.27e-26	59
monocyte	2.27e-26	59
monoblast	2.27e-26	59
promonocyte	2.27e-26	59
classical monocyte	2.94e-25	42
CD14-positive, CD16-negative classical monocyte	2.94e-25	42
granulocyte monocyte progenitor cell	1.35e-23	67
myeloid lineage restricted progenitor cell	7.00e-22	66
myeloid cell	1.81e-16	108
common myeloid progenitor	1.81e-16	108
mesenchymal cell	1.04e-15	354
connective tissue cell	5.69e-15	361
multi fate stem cell	3.68e-13	427
lymphocyte	5.11e-13	53
common lymphoid progenitor	5.11e-13	53
lymphoid lineage restricted progenitor cell	6.15e-13	52
somatic stem cell	1.29e-11	433
nucleate cell	2.36e-11	55
stem cell	5.67e-11	441
stuff accumulating cell	2.04e-09	87
motile cell	3.34e-09	386
mature alpha-beta T cell	3.46e-09	18
alpha-beta T cell	3.46e-09	18
immature T cell	3.46e-09	18
mature T cell	3.46e-09	18
immature alpha-beta T cell	3.46e-09	18
T cell	5.78e-08	25
pro-T cell	5.78e-08	25

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	3.78e-29	108
hematopoietic system	6.19e-29	98
blood island	6.19e-29	98
immune system	2.32e-22	93
bone marrow	3.36e-21	76
bone element	1.21e-17	82
connective tissue	8.02e-15	371
skeletal element	1.36e-14	90
lateral plate mesoderm	1.31e-13	203
skeletal system	1.06e-12	100
mesoderm	6.15e-09	315
mesoderm-derived structure	6.15e-09	315
presumptive mesoderm	6.15e-09	315
musculoskeletal system	1.45e-08	167
blood	4.97e-08	15
haemolymphatic fluid	4.97e-08	15
organism substance	4.97e-08	15

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
CTCF#10664	10	2.82118756477633	0.00089703736288379	0.00667562242712128
POLR2A#5430	18	2.03442932516028	1.12471092130166e-05	0.000287760127167623
RFX5#5993	6	3.80460341911424	0.00343118508361132	0.0174608750644293
WRNIP1#56897	2	11.5599962473027	0.0127864612829103	0.0460103786495957

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.