Coexpression cluster:C890

Full id: C890_CD19_CD4_Peripheral_CD8_Natural_Dendritic_Mast

Phase1 CAGE Peaks

Hg19::chr12:12510270..12510289,+	p5@LOH12CR1
Hg19::chr12:133065939..133065959,+	p6@FBRSL1
Hg19::chr17:76356237..76356282,-	p2@SOCS3
Hg19::chr19:54041603..54041615,+	p10@ZNF331
Hg19::chr19:54041645..54041661,+	p5@ZNF331
Hg19::chr20:34203794..34203818,+	p8@SPAG4
Hg19::chrX:110924471..110924482,+	p5@ALG13
Hg19::chrX:110924562..110924571,+	p8@ALG13
Hg19::chrX:110924578..110924589,+	p9@ALG13

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:0004577	N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity	0.0150712351348169
GO:0046627	negative regulation of insulin receptor signaling pathway	0.0188357167392016
GO:0030259	lipid glycosylation	0.0188357167392016
GO:0046626	regulation of insulin receptor signaling pathway	0.0188357167392016

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	7.84e-42	42
CD14-positive, CD16-negative classical monocyte	7.84e-42	42
leukocyte	2.11e-38	136
myeloid leukocyte	1.34e-35	72
defensive cell	1.39e-34	48
phagocyte	1.39e-34	48
granulocyte monocyte progenitor cell	1.07e-30	67
hematopoietic lineage restricted progenitor cell	1.33e-29	120
myeloid lineage restricted progenitor cell	3.84e-28	66
macrophage dendritic cell progenitor	4.21e-28	61
nongranular leukocyte	4.53e-28	115
hematopoietic stem cell	2.02e-27	168
angioblastic mesenchymal cell	2.02e-27	168
hematopoietic cell	3.14e-27	177
monopoietic cell	2.98e-26	59
monocyte	2.98e-26	59
monoblast	2.98e-26	59
promonocyte	2.98e-26	59
hematopoietic oligopotent progenitor cell	1.87e-23	161
hematopoietic multipotent progenitor cell	1.87e-23	161
myeloid cell	1.78e-20	108
common myeloid progenitor	1.78e-20	108
stuff accumulating cell	2.24e-13	87
intermediate monocyte	1.68e-09	9
CD14-positive, CD16-positive monocyte	1.68e-09	9
CD4-positive, alpha-beta T cell	5.15e-09	6
granulocyte	1.70e-07	8
circulating cell	5.05e-07	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	3.31e-28	98
blood island	3.31e-28	98
bone marrow	3.94e-27	76
bone element	4.10e-25	82
hemolymphoid system	8.57e-25	108
immune system	2.65e-24	93
skeletal element	2.46e-21	90
skeletal system	1.61e-17	100
adult organism	1.14e-08	114
lateral plate mesoderm	3.14e-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
CTCF#10664	6	3.57350424871668	0.00210388362937215	0.0121651811741777
CTCFL#140690	4	8.77621082621082	0.000674068038261004	0.00543915567086001
E2F6#1876	7	3.90223223576463	0.000306742359949273	0.00316185011160108
EGR1#1958	8	4.43393697316457	1.92853122912633e-05	0.000435395315691148
ELK4#2005	4	7.21585851487468	0.00140953905898738	0.0091651631043197
GABPB1#2553	5	3.92649102010121	0.00433797609228731	0.0205840020491774
GTF2F1#2962	5	7.07758937597647	0.000286543585358045	0.00304686677980135
HEY1#23462	7	3.14230858908222	0.00125876346284377	0.0084575397128114
JUND#3727	6	4.66310929458068	0.000484968200539146	0.00433755193081338
MYC#4609	6	3.4815212477396	0.00242366981145926	0.0136551573306896
PAX5#5079	6	4.44637702078522	0.000632270008817587	0.00519091639422215
POLR2A#5430	8	1.90884726805162	0.011661228959883	0.0425789984037065
POU2F2#5452	4	4.04716624788557	0.0116142615615323	0.0424342089636127
RAD21#5885	4	4.60223728686948	0.00735124290019625	0.0303953623363394
SETDB1#9869	3	13.4400087260035	0.00114472325146679	0.00783702075778038
SMARCB1#6598	3	6.08423859371914	0.0107567140124601	0.0396968358567958
TAF1#6872	8	2.97159669844026	0.000423374995123481	0.00395853725297236
TFAP2C#7022	4	4.80410160438232	0.00629930343474712	0.0277861617359274
USF1#7391	6	4.24099951813864	0.000822001744194416	0.00625949982952392
ZEB1#6935	3	5.62947733918129	0.0133048823634195	0.0470347835071986
ZNF143#7702	5	7.50048697345995	0.000217746517580183	0.00249137034942558

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.