Coexpression cluster:C936

Full id: C936_CD4_CD14_granulocyte_CD14CD16_CD8_Dendritic_Hair

Phase1 CAGE Peaks

Hg19::chr20:35580040..35580066,-	p3@SAMHD1
Hg19::chr20:35580068..35580094,-	p1@SAMHD1
Hg19::chr20:35580104..35580133,-	p2@SAMHD1
Hg19::chr20:35580152..35580163,-	p5@SAMHD1
Hg19::chr20:35580173..35580200,-	p4@SAMHD1
Hg19::chr20:35580214..35580223,-	p7@SAMHD1
Hg19::chr20:35580240..35580251,-	p6@SAMHD1
Hg19::chr7:142960556..142960600,+	p1@GSTK1
Hg19::chr9:4985246..4985329,+	p1@JAK2

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

---

No results for this coexpression

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:0030288	outer membrane-bounded periplasmic space	0.0115035799203901
GO:0030313	cell envelope	0.0115035799203901
GO:0044462	external encapsulating structure part	0.0115035799203901
GO:0007262	STAT protein nuclear translocation	0.0115035799203901
GO:0004718	Janus kinase activity	0.0115035799203901
GO:0042597	periplasmic space	0.0115035799203901
GO:0030312	external encapsulating structure	0.0115035799203901
GO:0004716	receptor signaling protein tyrosine kinase activity	0.0196075728125403
GO:0004602	glutathione peroxidase activity	0.0196075728125403
GO:0015035	protein disulfide oxidoreductase activity	0.0196075728125403
GO:0042169	SH2 domain binding	0.0196075728125403
GO:0007260	tyrosine phosphorylation of STAT protein	0.0196075728125403
GO:0006749	glutathione metabolic process	0.0196075728125403
GO:0015036	disulfide oxidoreductase activity	0.0196746334083543
GO:0000060	protein import into nucleus, translocation	0.0196746334083543
GO:0007259	JAK-STAT cascade	0.0280287321429359
GO:0004715	non-membrane spanning protein tyrosine kinase activity	0.0280287321429359
GO:0018108	peptidyl-tyrosine phosphorylation	0.0280287321429359
GO:0018212	peptidyl-tyrosine modification	0.0280287321429359
GO:0004364	glutathione transferase activity	0.0280287321429359
GO:0007498	mesoderm development	0.0280287321429359
GO:0045121	lipid raft	0.0280287321429359
GO:0002376	immune system process	0.0320820002381753
GO:0004601	peroxidase activity	0.0359033090866457
GO:0016684	oxidoreductase activity, acting on peroxide as acceptor	0.0359033090866457
GO:0030099	myeloid cell differentiation	0.0396633258639042
GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	0.0411241581148477
GO:0006790	sulfur metabolic process	0.0411241581148477
GO:0006606	protein import into nucleus	0.0418241842302334
GO:0051170	nuclear import	0.0418241842302334
GO:0042579	microbody	0.0418241842302334
GO:0005777	peroxisome	0.0418241842302334
GO:0018193	peptidyl-amino acid modification	0.0479928798143188
GO:0017038	protein import	0.0479928798143188
GO:0019904	protein domain specific binding	0.0485252268225351

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	2.27e-31	136
nongranular leukocyte	1.43e-30	115
macrophage dendritic cell progenitor	8.81e-29	61
myeloid leukocyte	1.74e-28	72
monopoietic cell	1.99e-28	59
monocyte	1.99e-28	59
monoblast	1.99e-28	59
promonocyte	1.99e-28	59
granulocyte monocyte progenitor cell	5.76e-28	67
hematopoietic lineage restricted progenitor cell	4.00e-27	120
hematopoietic stem cell	3.92e-25	168
angioblastic mesenchymal cell	3.92e-25	168
defensive cell	5.33e-25	48
phagocyte	5.33e-25	48
myeloid lineage restricted progenitor cell	2.70e-24	66
hematopoietic oligopotent progenitor cell	5.02e-23	161
hematopoietic multipotent progenitor cell	5.02e-23	161
hematopoietic cell	3.75e-22	177
classical monocyte	1.23e-21	42
CD14-positive, CD16-negative classical monocyte	1.23e-21	42
myeloid cell	1.85e-18	108
common myeloid progenitor	1.85e-18	108
stuff accumulating cell	1.09e-16	87
mature alpha-beta T cell	1.87e-09	18
alpha-beta T cell	1.87e-09	18
immature T cell	1.87e-09	18
mature T cell	1.87e-09	18
immature alpha-beta T cell	1.87e-09	18

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.43e-30	98
blood island	2.43e-30	98
hemolymphoid system	3.85e-30	108
immune system	1.69e-25	93
bone marrow	6.38e-24	76
adult organism	3.58e-22	114
bone element	2.78e-19	82
skeletal element	2.37e-18	90
skeletal system	1.13e-16	100
lateral plate mesoderm	1.24e-09	203
musculoskeletal system	2.52e-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

---

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

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	7	17.4713579646735	1.14940906869096e-08	8.6237883423143e-07
CTCF#10664	8	4.76467233162225	1.10088565904027e-05	0.000285015858563477
CTCFL#140690	8	17.5524216524216	3.70770685210878e-10	3.6914127352468e-08
E2F1#1869	8	4.3621237465594	2.18983367577486e-05	0.000481279543906252
E2F4#1874	7	9.85293580077679	5.95188909661047e-07	2.73716136222326e-05
E2F6#1876	9	5.01715573169739	4.96068808485209e-07	2.32431270925916e-05
HEY1#23462	9	4.04011104310571	3.4850025352467e-06	0.000115987947666868
HMGN3#9324	8	7.26982019853386	4.00320733604597e-07	1.93560634708012e-05
JUN#3725	7	9.73220048292826	6.47658215823223e-07	2.93834823641883e-05
MXI1#4601	7	7.74788904459056	3.07469224127045e-06	0.000103720214142779
NANOG#79923	7	22.7459388185654	1.84595149658852e-09	1.59991143860754e-07
NRF1#4899	9	12.2102794477109	1.65394511709215e-10	1.73604396064308e-08
PAX5#5079	5	3.70531418398768	0.00561655707771942	0.0253945021273621
PBX3#5090	7	17.0446209785788	1.36394115359822e-08	1.00315950803271e-06
POLR2A#5430	9	2.14745317655807	0.00102941289260802	0.00728887139600606
RFX5#5993	7	9.37059731004063	8.3937256470655e-07	3.65111333966628e-05
SIN3A#25942	8	4.80789753494679	1.02597602607548e-05	0.000268080836095314
TAF1#6872	9	3.34304628574529	1.91655056102793e-05	0.000433533948544935
TBP#6908	9	3.70677068709639	7.56501052505806e-06	0.000215928432420481
TCF7L2#6934	7	8.37680399355127	1.80610965338292e-06	6.77300847718704e-05
TFAP2A#7020	8	14.6832305538177	1.5325776526732e-09	1.35415293965767e-07
TFAP2C#7022	8	9.60820320876464	4.42575919806395e-08	2.89794272656176e-06
THAP1#55145	7	24.3982235799955	1.13434844000145e-09	1.04195441271162e-07
ZEB1#6935	3	5.62947733918129	0.0133048823634195	0.0470379678803415

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.