Coexpression cluster:C426

Full id: C426_CD4_CD14_Neutrophils_CD8_Natural_Mast_Eosinophils

Phase1 CAGE Peaks

Hg19::chr14:35871591..35871602,-	p@chr14:35871591..35871602 -
Hg19::chr4:103480333..103480371,+	p@chr4:103480333..103480371 +
Hg19::chr4:103496453..103496481,+	p@chr4:103496453..103496481 +
Hg19::chr4:103498478..103498489,+	p12@NFKB1
Hg19::chr4:103498623..103498650,+	p9@NFKB1
Hg19::chr6:138189104..138189115,+	p@chr6:138189104..138189115 +
Hg19::chr6:138189215..138189247,+	p@chr6:138189215..138189247 +
Hg19::chr6:138190239..138190250,+	p@chr6:138190239..138190250 +
Hg19::chr6:138192331..138192343,+	p10@TNFAIP3
Hg19::chr6:138192345..138192366,+	p11@TNFAIP3
Hg19::chr6:138192426..138192438,+	p12@TNFAIP3
Hg19::chr6:138192543..138192555,+	p13@TNFAIP3
Hg19::chr6:138196020..138196034,+	p8@TNFAIP3
Hg19::chr6:138196838..138196867,+	p16@TNFAIP3
Hg19::chr6:138197180..138197238,+	p9@TNFAIP3
Hg19::chr6:138198202..138198217,+	p@chr6:138198202..138198217 +
Hg19::chr6:138198297..138198311,+	p@chr6:138198297..138198311 +
Hg19::chr6:138198346..138198366,+	p@chr6:138198346..138198366 +
Hg19::chr6:138199895..138199908,+	p@chr6:138199895..138199908 +
Hg19::chr6:138199945..138199956,+	p@chr6:138199945..138199956 +
Hg19::chr6:138201273..138201294,+	p@chr6:138201273..138201294 +
Hg19::chr6:138204018..138204028,+	p@chr6:138204018..138204028 +
Hg19::chr6:138204056..138204068,+	p@chr6:138204056..138204068 +
Hg19::chr7:138766106..138766122,-	p@chr7:138766106..138766122 -

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.value	FDR	nGenes	nPathway	Name
4.19956876000442e-06	0.0026583270250828	2	59	NOD-like receptor signaling pathway (KEGG):04621
2.18716290008179e-05	0.00405227851947455	2	134	Measles (KEGG):05162
0.000770550915555693	0.0487758729546754	1	11	Osteopontin Signaling (Wikipathways):WP1434
2.38818258532104e-05	0.00405227851947455	2	140	Regulation of toll-like receptor signaling pathway (Wikipathways):WP1449
0.00056043011929242	0.0443440331890127	1	8	TFs Regulate miRNAs related to cardiac hypertrophy (Wikipathways):WP1559
4.31443715156972e-05	0.00455173119490606	2	188	TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231
0.000319827473566556	0.0289215415382328	2	511	Signaling in Immune system (Reactome):REACT_6900
0.00064951693852861	0.0456826913431789	2	728	TNF alpha/NF-kB up reg. targets (Netpath):NetPath_9
3.20085191111734e-05	0.00405227851947455	2	162	TNF alpha/NF-kB down reg. targets (Netpath):NetPath_9
2.92938943019595e-05	0.00405227851947455	2	155	IL-1 up reg. targets (Netpath):NetPath_13

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 ID	GO name	FDR corrected p-value
GO:0006916	anti-apoptosis	0.0012626724630421
GO:0043066	negative regulation of apoptosis	0.0012626724630421
GO:0043069	negative regulation of programmed cell death	0.0012626724630421
GO:0042981	regulation of apoptosis	0.00476396946754751
GO:0043067	regulation of programmed cell death	0.00476396946754751
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.00488601741722185
GO:0006915	apoptosis	0.00592300066246309
GO:0012501	programmed cell death	0.00592300066246309
GO:0016265	death	0.00592300066246309
GO:0008219	cell death	0.00592300066246309
GO:0048523	negative regulation of cellular process	0.00836632581832125
GO:0048519	negative regulation of biological process	0.00836632581832125
GO:0048468	cell development	0.00852704727292275
GO:0048869	cellular developmental process	0.0156990917752577
GO:0030154	cell differentiation	0.0156990917752577
GO:0009968	negative regulation of signal transduction	0.030993977189682
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.030993977189682
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0376570466175902
GO:0032502	developmental process	0.0423912959518589
GO:0003677	DNA binding	0.0441894487628634

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 term	p-value	n
leukocyte	3.95e-58	136
hematopoietic cell	6.93e-43	177
hematopoietic lineage restricted progenitor cell	1.80e-42	120
hematopoietic stem cell	2.34e-42	168
angioblastic mesenchymal cell	2.34e-42	168
nongranular leukocyte	1.48e-41	115
classical monocyte	6.40e-41	42
CD14-positive, CD16-negative classical monocyte	6.40e-41	42
hematopoietic oligopotent progenitor cell	1.01e-40	161
hematopoietic multipotent progenitor cell	1.01e-40	161
myeloid leukocyte	4.32e-39	72
defensive cell	2.91e-34	48
phagocyte	2.91e-34	48
granulocyte monocyte progenitor cell	7.56e-31	67
macrophage dendritic cell progenitor	3.94e-29	61
myeloid lineage restricted progenitor cell	8.15e-28	66
myeloid cell	3.02e-27	108
common myeloid progenitor	3.02e-27	108
monopoietic cell	1.03e-26	59
monocyte	1.03e-26	59
monoblast	1.03e-26	59
promonocyte	1.03e-26	59
mesenchymal cell	1.67e-16	354
connective tissue cell	1.08e-15	361
stuff accumulating cell	1.11e-14	87
granulocyte	3.32e-13	8
motile cell	7.21e-13	386
lymphoid lineage restricted progenitor cell	2.06e-12	52
lymphocyte	4.84e-12	53
common lymphoid progenitor	4.84e-12	53
blood cell	1.95e-11	11
nucleate cell	2.42e-11	55
multi fate stem cell	5.60e-11	427
somatic stem cell	6.20e-11	433
stem cell	8.15e-11	441
CD4-positive, alpha-beta T cell	1.71e-10	6
circulating cell	2.75e-09	6
mature alpha-beta T cell	8.66e-08	18
alpha-beta T cell	8.66e-08	18
immature T cell	8.66e-08	18
mature T cell	8.66e-08	18
immature alpha-beta T cell	8.66e-08	18
Langerhans cell	8.98e-08	5
T cell	4.28e-07	25
pro-T cell	4.28e-07	25

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.35e-30	98
blood island	1.35e-30	98
hemolymphoid system	1.68e-27	108
bone marrow	1.24e-25	76
immune system	1.44e-25	93
bone element	8.32e-23	82
skeletal element	1.21e-19	90
skeletal system	1.76e-17	100
connective tissue	1.36e-14	371
lateral plate mesoderm	7.37e-10	203
musculoskeletal system	6.15e-07	167

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

---

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

---

This analysis result is provided for C0 - C305 clusters.