Coexpression cluster:C739

Full id: C739_granulocyte_CD34_CD19_CD14CD16_CD4_Mesothelial_Dendritic

Phase1 CAGE Peaks

Hg19::chr11:5248320..5248322,+	p@chr11:5248320..5248322 +
Hg19::chr15:39872100..39872101,-	p@chr15:39872100..39872101 -
Hg19::chr17:37864788..37864790,-	p@chr17:37864788..37864790 -
Hg19::chr17:7145967..7145970,+	p@chr17:7145967..7145970 +
Hg19::chr19:39786962..39786965,+	p2@IL29
Hg19::chr19:39786984..39786986,-	p@chr19:39786984..39786986 -
Hg19::chr1:36786251..36786257,+	p12@SH3D21
Hg19::chr20:62243927..62243929,+	p@chr20:62243927..62243929 +
Hg19::chr21:34143971..34143983,-	p8@GCFC1
Hg19::chr6:111580680..111580691,+	p3@KIAA1919
Hg19::chr8:104151242..104151262,+	p@chr8:104151242..104151262 +

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:0032003	interleukin-28 receptor binding	0.00426815806625265
GO:0045345	positive regulation of MHC class I biosynthetic process	0.00426815806625265
GO:0045341	MHC class I biosynthetic process	0.00426815806625265
GO:0045343	regulation of MHC class I biosynthetic process	0.00426815806625265
GO:0032002	interleukin-28 receptor complex	0.00512171429365841
GO:0046427	positive regulation of JAK-STAT cascade	0.00853568791713221
GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein	0.00853568791713221
GO:0042509	regulation of tyrosine phosphorylation of STAT protein	0.0128014587649671
GO:0046425	regulation of JAK-STAT cascade	0.0128014587649671
GO:0051607	defense response to virus	0.0128014587649671
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	0.0128014587649671
GO:0007260	tyrosine phosphorylation of STAT protein	0.0128014587649671
GO:0042327	positive regulation of phosphorylation	0.013273632419546
GO:0045937	positive regulation of phosphate metabolic process	0.013273632419546
GO:0001934	positive regulation of protein amino acid phosphorylation	0.013273632419546
GO:0033240	positive regulation of amine metabolic process	0.013273632419546
GO:0045764	positive regulation of amino acid metabolic process	0.013273632419546
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.013273632419546
GO:0007259	JAK-STAT cascade	0.0163506766880092
GO:0018108	peptidyl-tyrosine phosphorylation	0.0163506766880092
GO:0018212	peptidyl-tyrosine modification	0.0163506766880092
GO:0001932	regulation of protein amino acid phosphorylation	0.0163506766880092
GO:0033238	regulation of amine metabolic process	0.0163506766880092
GO:0006521	regulation of amino acid metabolic process	0.0163506766880092
GO:0045727	positive regulation of translation	0.0180834056716837
GO:0031328	positive regulation of cellular biosynthetic process	0.0192562602658128
GO:0042325	regulation of phosphorylation	0.0192562602658128
GO:0016324	apical plasma membrane	0.0192562602658128
GO:0051174	regulation of phosphorus metabolic process	0.0192562602658128
GO:0019220	regulation of phosphate metabolic process	0.0192562602658128
GO:0009891	positive regulation of biosynthetic process	0.0192562602658128
GO:0044459	plasma membrane part	0.0198232630492858
GO:0050778	positive regulation of immune response	0.0198232630492858
GO:0051247	positive regulation of protein metabolic process	0.0198232630492858
GO:0045177	apical part of cell	0.0198232630492858
GO:0002684	positive regulation of immune system process	0.0198232630492858
GO:0005351	sugar:hydrogen ion symporter activity	0.0198232630492858
GO:0051119	sugar transmembrane transporter activity	0.0198232630492858
GO:0031402	sodium ion binding	0.0198232630492858
GO:0015144	carbohydrate transmembrane transporter activity	0.0198232630492858
GO:0050776	regulation of immune response	0.0198232630492858
GO:0009615	response to virus	0.0198232630492858
GO:0002682	regulation of immune system process	0.0198232630492858
GO:0051240	positive regulation of multicellular organismal process	0.020127892237198
GO:0043235	receptor complex	0.020127892237198
GO:0002252	immune effector process	0.020127892237198
GO:0008643	carbohydrate transport	0.020127892237198
GO:0018193	peptidyl-amino acid modification	0.0214809399458696
GO:0009967	positive regulation of signal transduction	0.0265949721698051
GO:0006814	sodium ion transport	0.0294613158369408
GO:0006417	regulation of translation	0.0307151888842789
GO:0031326	regulation of cellular biosynthetic process	0.0325731024021994
GO:0051707	response to other organism	0.0330792660137437
GO:0005886	plasma membrane	0.0335730676928623
GO:0009889	regulation of biosynthetic process	0.0335730676928623
GO:0031420	alkali metal ion binding	0.0335853857639441
GO:0008285	negative regulation of cell proliferation	0.0335853857639441
GO:0015293	symporter activity	0.0354912267981477
GO:0051239	regulation of multicellular organismal process	0.0395320354538901
GO:0045941	positive regulation of transcription	0.0395320354538901
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.039622163689615
GO:0009607	response to biotic stimulus	0.039622163689615
GO:0005125	cytokine activity	0.041813676195433
GO:0051704	multi-organism process	0.0441991330548567
GO:0015291	secondary active transmembrane transporter activity	0.0469561865029264
GO:0031325	positive regulation of cellular metabolic process	0.0469561865029264
GO:0007243	protein kinase cascade	0.0476415885686142
GO:0009893	positive regulation of metabolic process	0.0488027856147575

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><br><br>

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Cell Type

Ontology term	p-value	n
plasmacytoid dendritic cell	1.79e-17	3
CD34-positive, CD38-negative hematopoietic stem cell	5.15e-14	1
CD4-positive, alpha-beta thymocyte	1.10e-13	1
naive thymus-derived CD4-positive, alpha-beta T cell	1.10e-13	1
mature CD4 single-positive thymocyte	1.10e-13	1
resting double-positive thymocyte	1.10e-13	1
double-positive blast	1.10e-13	1
CD69-positive double-positive thymocyte	1.10e-13	1
CD69-positive, CD4-positive single-positive thymocyte	1.10e-13	1
CD4-positive, CD8-intermediate double-positive thymocyte	1.10e-13	1
CD24-positive, CD4 single-positive thymocyte	1.10e-13	1
B cell	1.09e-08	14
hematopoietic stem cell	1.44e-07	168
angioblastic mesenchymal cell	1.44e-07	168
thymocyte	1.75e-07	2
double negative thymocyte	1.75e-07	2
double-positive, alpha-beta thymocyte	1.75e-07	2
DN4 thymocyte	1.75e-07	2
DN1 thymic pro-T cell	1.75e-07	2
DN2 thymocyte	1.75e-07	2
DN3 thymocyte	1.75e-07	2
immature single positive thymocyte	1.75e-07	2
early T lineage precursor	1.75e-07	2
hematopoietic cell	4.13e-07	177

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
STAT1#6772	3	5.64725113559978	0.0138689600283293	0.0487188562913687
STAT2#6773	2	11.8661402157165	0.01177528842153	0.0429054651451759
XRCC4#7518	1	390.754756871036	0.00255624412618194	0.0141456885653746

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.