Coexpression cluster:C250

Full id: C250_Mast_Neutrophils_CD14_Eosinophils_CD8_Peripheral_CD4

Phase1 CAGE Peaks

Hg19::chr10:3826687..3826699,-	p@chr10:3826687..3826699 -
Hg19::chr16:27325702..27325750,-	p@chr16:27325702..27325750 -
Hg19::chr16:27325969..27325994,+	p@chr16:27325969..27325994 +
Hg19::chr17:38506028..38506044,+	p@chr17:38506028..38506044 +
Hg19::chr19:13264446..13264492,+	p3@IER2
Hg19::chr19:13953130..13953158,-	p@chr19:13953130..13953158 -
Hg19::chr19:39897051..39897070,+	p3@ZFP36
Hg19::chr19:39898470..39898488,+	p@chr19:39898470..39898488 +
Hg19::chr19:39898498..39898514,+	p@chr19:39898498..39898514 +
Hg19::chr19:39898523..39898532,+	p@chr19:39898523..39898532 +
Hg19::chr19:39898544..39898598,+	p@chr19:39898544..39898598 +
Hg19::chr19:39898599..39898666,+	p@chr19:39898599..39898666 +
Hg19::chr19:39898678..39898692,-	p@chr19:39898678..39898692 -
Hg19::chr19:39898695..39898725,-	p@chr19:39898695..39898725 -
Hg19::chr19:39898701..39898712,+	p@chr19:39898701..39898712 +
Hg19::chr19:39898715..39898729,+	p@chr19:39898715..39898729 +
Hg19::chr19:39898746..39898756,+	p@chr19:39898746..39898756 +
Hg19::chr19:39898760..39898777,+	p@chr19:39898760..39898777 +
Hg19::chr19:39898772..39898888,-	p1@CU679444
Hg19::chr19:39898781..39898796,+	p@chr19:39898781..39898796 +
Hg19::chr19:39898814..39898855,+	p@chr19:39898814..39898855 +
Hg19::chr19:39898896..39898901,+	p@chr19:39898896..39898901 +
Hg19::chr19:39898940..39898958,+	p@chr19:39898940..39898958 +
Hg19::chr19:39898968..39898980,+	p@chr19:39898968..39898980 +
Hg19::chr19:39898988..39899013,+	p@chr19:39898988..39899013 +
Hg19::chr19:39899024..39899036,+	p@chr19:39899024..39899036 +
Hg19::chr19:39899079..39899097,+	p@chr19:39899079..39899097 +
Hg19::chr19:39899258..39899276,+	p@chr19:39899258..39899276 +
Hg19::chr19:39899297..39899308,+	p@chr19:39899297..39899308 +
Hg19::chr19:39899540..39899551,+	p2@AJ227917
Hg19::chr19:39899566..39899574,-	p8@CU679444
Hg19::chr19:39899597..39899634,+	p1@AJ227917
Hg19::chr19:39899887..39899894,+	p4@AJ227917
Hg19::chr1:204380074..204380108,-	p8@PPP1R15B
Hg19::chr3:128445232..128445249,+	p@chr3:128445232..128445249 +
Hg19::chr3:39186740..39186774,-	p@chr3:39186740..39186774 -
Hg19::chr3:39188204..39188217,-	p3@CU691620
Hg19::chr5:172195219..172195236,-	p3@AJ227912
Hg19::chr5:172195778..172195809,+	p@chr5:172195778..172195809 +
Hg19::chr5:172195833..172195881,-	p2@AJ227912
Hg19::chr5:172195883..172195911,-	p4@AJ227912
Hg19::chr5:172195926..172195937,-	p13@AJ227912
Hg19::chr5:172195979..172196000,-	p6@AJ227912
Hg19::chr5:172196072..172196092,-	p5@AJ227912
Hg19::chr5:172196095..172196120,-	p1@AJ227912
Hg19::chr5:172196608..172196676,-	p@chr5:172196608..172196676 -
Hg19::chr5:172196683..172196802,-	p@chr5:172196683..172196802 -
Hg19::chr5:172197180..172197212,-	p2@AK127679
Hg19::chr5:172197219..172197279,-	p1@AK127679
Hg19::chr5:172197282..172197310,-	p3@AK127679
Hg19::chr6:35310813..35310823,+	p@chr6:35310813..35310823 +
Hg19::chr8:38645035..38645076,+	p11@TACC1

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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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

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GO ID	GO name	FDR corrected p-value
GO:0017091	AU-rich element binding	0.00447427293064877
GO:0000289	poly(A) tail shortening	0.00447427293064877
GO:0050779	RNA destabilization	0.00447427293064877
GO:0000288	mRNA catabolic process, deadenylation-dependent decay	0.0134180779336029
GO:0043487	regulation of RNA stability	0.0134180779336029
GO:0043488	regulation of mRNA stability	0.0134180779336029
GO:0004726	non-membrane spanning protein tyrosine phosphatase activity	0.0134180779336029
GO:0031348	negative regulation of defense response	0.0134180779336029
GO:0050728	negative regulation of inflammatory response	0.0134180779336029
GO:0031124	mRNA 3'-end processing	0.0167644521049474
GO:0033549	MAP kinase phosphatase activity	0.0167644521049474
GO:0017017	MAP kinase tyrosine/serine/threonine phosphatase activity	0.0167644521049474
GO:0045638	negative regulation of myeloid cell differentiation	0.0167644521049474
GO:0031123	RNA 3'-end processing	0.0167644521049474
GO:0051252	regulation of RNA metabolic process	0.0167644521049474
GO:0003727	single-stranded RNA binding	0.0167644521049474
GO:0031347	regulation of defense response	0.0186230565034739
GO:0050727	regulation of inflammatory response	0.0186230565034739
GO:0006402	mRNA catabolic process	0.0201572588362358
GO:0007049	cell cycle	0.0201572588362358
GO:0045637	regulation of myeloid cell differentiation	0.0203953832529684
GO:0003729	mRNA binding	0.0203953832529684
GO:0048583	regulation of response to stimulus	0.0203953832529684
GO:0006401	RNA catabolic process	0.0256759940779331
GO:0006950	response to stress	0.032222988276366
GO:0008138	protein tyrosine/serine/threonine phosphatase activity	0.032222988276366
GO:0045596	negative regulation of cell differentiation	0.032222988276366
GO:0030099	myeloid cell differentiation	0.035520473619963
GO:0051093	negative regulation of developmental process	0.035520473619963

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
classical monocyte	2.00e-33	42
CD14-positive, CD16-negative classical monocyte	2.00e-33	42
defensive cell	4.76e-28	48
phagocyte	4.76e-28	48
myeloid leukocyte	7.43e-27	72
leukocyte	1.71e-24	136
granulocyte monocyte progenitor cell	2.21e-21	67
macrophage dendritic cell progenitor	5.84e-21	61
monopoietic cell	1.31e-19	59
monocyte	1.31e-19	59
monoblast	1.31e-19	59
promonocyte	1.31e-19	59
myeloid lineage restricted progenitor cell	1.94e-19	66
hematopoietic lineage restricted progenitor cell	8.83e-17	120
nongranular leukocyte	1.35e-16	115
stuff accumulating cell	2.49e-15	87
hematopoietic stem cell	8.27e-14	168
angioblastic mesenchymal cell	8.27e-14	168
myeloid cell	3.72e-13	108
common myeloid progenitor	3.72e-13	108
hematopoietic cell	1.52e-12	177
hematopoietic oligopotent progenitor cell	2.21e-12	161
hematopoietic multipotent progenitor cell	2.21e-12	161
granulocyte	1.86e-08	8
intermediate monocyte	3.71e-08	9
CD14-positive, CD16-positive monocyte	3.71e-08	9
connective tissue cell	7.17e-07	361

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.95e-25	98
blood island	6.95e-25	98
hemolymphoid system	1.73e-22	108
bone marrow	4.07e-19	76
immune system	1.37e-17	93
skeletal element	1.55e-17	90
bone element	3.47e-17	82
skeletal system	8.22e-16	100
adult organism	1.31e-12	114
lateral plate mesoderm	3.05e-08	203

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
CCNT2#905	15	1.82775045489307	0.0124007378113127	0.0448930866330094
EBF1#1879	23	3.93939879752091	1.8712595866431e-09	1.61915890612609e-07
HEY1#23462	21	1.63158330586961	0.00936700342956532	0.0353514426039957
PAX5#5079	20	2.56521751199147	3.10097941821131e-05	0.000628250610006927
POLR2A#5430	50	2.06485882361353	9.85681600402904e-15	1.70719072412071e-12
USF2#7392	26	6.4960986925348	7.30629970006958e-16	1.38486866492843e-13

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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