Coexpression cluster:C306

Full id: C306_CD4_CD8_Neutrophils_Natural_CD19_CD14_Peripheral

Phase1 CAGE Peaks

Hg19::chr10:112662692..112662695,+	p@chr10:112662692..112662695 +
Hg19::chr10:120969026..120969030,+	p@chr10:120969026..120969030 +
Hg19::chr10:70101463..70101469,+	p14@HNRNPH3
Hg19::chr11:64540106..64540118,-	p@chr11:64540106..64540118 -
Hg19::chr11:66412411..66412415,+	p@chr11:66412411..66412415 +
Hg19::chr12:496389..496393,-	p@chr12:496389..496393 -
Hg19::chr12:92506284..92506289,-	p@chr12:92506284..92506289 -
Hg19::chr12:92517978..92517981,-	p@chr12:92517978..92517981 -
Hg19::chr12:92521923..92521946,-	p@chr12:92521923..92521946 -
Hg19::chr12:92525764..92525779,-	p@chr12:92525764..92525779 -
Hg19::chr12:92529815..92529831,-	p@chr12:92529815..92529831 -
Hg19::chr16:2805857..2805868,+	p3@AB384460
Hg19::chr16:31196235..31196241,+	p@chr16:31196235..31196241 +
Hg19::chr17:38720548..38720562,-	p@chr17:38720548..38720562 -
Hg19::chr17:8397217..8397222,+	p@chr17:8397217..8397222 +
Hg19::chr18:2734660..2734665,+	p@chr18:2734660..2734665 +
Hg19::chr18:9218683..9218688,+	p@chr18:9218683..9218688 +
Hg19::chr1:14076901..14076905,+	p@chr1:14076901..14076905 +
Hg19::chr1:14084295..14084298,+	p@chr1:14084295..14084298 +
Hg19::chr1:171519143..171519147,+	p@chr1:171519143..171519147 +
Hg19::chr20:34304613..34304617,-	p@chr20:34304613..34304617 -
Hg19::chr20:42837055..42837068,-	p@chr20:42837055..42837068 -
Hg19::chr21:34931287..34931294,+	p@chr21:34931287..34931294 +
Hg19::chr2:238604341..238604365,+	p@chr2:238604341..238604365 +
Hg19::chr2:30378335..30378347,+	p@chr2:30378335..30378347 +
Hg19::chr2:47171535..47171539,+	p@chr2:47171535..47171539 +
Hg19::chr2:96959867..96959871,-	p@chr2:96959867..96959871 -
Hg19::chr3:119181738..119181740,-	p@chr3:119181738..119181740 -
Hg19::chr3:150332211..150332217,+	p@chr3:150332211..150332217 +
Hg19::chr3:156869602..156869621,-	p@chr3:156869602..156869621 -
Hg19::chr3:9932605..9932620,-	p@chr3:9932605..9932620 -
Hg19::chr4:103713093..103713096,-	p@chr4:103713093..103713096 -
Hg19::chr5:130638530..130638534,+	p@chr5:130638530..130638534 +
Hg19::chr5:32592687..32592708,+	p@chr5:32592687..32592708 +
Hg19::chr6:139489578..139489582,+	p@chr6:139489578..139489582 +
Hg19::chr7:26234405..26234412,-	p@chr7:26234405..26234412 -
Hg19::chr8:101725008..101725030,-	p16@PABPC1
Hg19::chr8:101728081..101728097,-	p22@PABPC1
Hg19::chr8:101959111..101959114,-	p@chr8:101959111..101959114 -

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:0043489	RNA stabilization	0.00193016097290205
GO:0048255	mRNA stabilization	0.00193016097290205
GO:0008494	translation activator activity	0.00193016097290205
GO:0008143	poly(A) binding	0.00193016097290205
GO:0043487	regulation of RNA stability	0.00193016097290205
GO:0043488	regulation of mRNA stability	0.00193016097290205
GO:0006378	mRNA polyadenylation	0.00193016097290205
GO:0043631	RNA polyadenylation	0.00233525648573335
GO:0031124	mRNA 3'-end processing	0.00233525648573335
GO:0031123	RNA 3'-end processing	0.00250206052042859
GO:0051252	regulation of RNA metabolic process	0.00250206052042859
GO:0003727	single-stranded RNA binding	0.00250206052042859
GO:0003729	mRNA binding	0.00392631035513409
GO:0005681	spliceosome	0.0149051319574103
GO:0008135	translation factor activity, nucleic acid binding	0.0201165665842458
GO:0008380	RNA splicing	0.0211111356411162
GO:0006397	mRNA processing	0.0241080890144825
GO:0016071	mRNA metabolic process	0.0285234899328859
GO:0006396	RNA processing	0.0414815296807897

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
leukocyte	2.23e-38	136
nongranular leukocyte	5.91e-35	115
hematopoietic stem cell	3.37e-33	168
angioblastic mesenchymal cell	3.37e-33	168
hematopoietic cell	3.56e-32	177
hematopoietic lineage restricted progenitor cell	4.51e-31	120
hematopoietic oligopotent progenitor cell	7.37e-31	161
hematopoietic multipotent progenitor cell	7.37e-31	161
classical monocyte	2.77e-26	42
CD14-positive, CD16-negative classical monocyte	2.77e-26	42
defensive cell	8.50e-22	48
phagocyte	8.50e-22	48
myeloid leukocyte	2.84e-20	72
lymphocyte	2.19e-16	53
common lymphoid progenitor	2.19e-16	53
monopoietic cell	5.34e-16	59
monocyte	5.34e-16	59
monoblast	5.34e-16	59
promonocyte	5.34e-16	59
lymphoid lineage restricted progenitor cell	6.10e-16	52
macrophage dendritic cell progenitor	8.91e-16	61
granulocyte monocyte progenitor cell	1.39e-15	67
myeloid lineage restricted progenitor cell	2.84e-15	66
nucleate cell	3.19e-15	55
myeloid cell	9.58e-15	108
common myeloid progenitor	9.58e-15	108
intermediate monocyte	1.95e-08	9
CD14-positive, CD16-positive monocyte	1.95e-08	9
T cell	1.99e-08	25
pro-T cell	1.99e-08	25
mature alpha-beta T cell	2.34e-07	18
alpha-beta T cell	2.34e-07	18
immature T cell	2.34e-07	18
mature T cell	2.34e-07	18
immature alpha-beta T cell	2.34e-07	18
CD4-positive, alpha-beta T cell	9.44e-07	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.05e-16	98
blood island	2.05e-16	98
hemolymphoid system	1.95e-13	108
bone marrow	1.90e-12	76
bone element	2.68e-11	82
immune system	4.70e-11	93
skeletal element	6.45e-09	90
skeletal system	1.95e-07	100

Disease

Ontology term	p-value	n
cell type cancer	1.54e-09	143
cancer	1.37e-08	235
disease of cellular proliferation	1.97e-08	239
carcinoma	2.25e-07	106

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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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

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This analysis result is provided for C0 - C305 clusters.