Coexpression cluster:C1039

Full id: C1039_CD4_NK_CD8_CD19_Natural_Whole_chronic

Phase1 CAGE Peaks

Hg19::chr14:91696341..91696361,+	p@chr14:91696341..91696361 +
Hg19::chr19:39225003..39225020,-	p@chr19:39225003..39225020 -
Hg19::chr2:191929516..191929561,+	p@chr2:191929516..191929561 +
Hg19::chr2:231792452..231792463,-	p@chr2:231792452..231792463 -
Hg19::chr4:110980983..110980988,-	p17@ELOVL6
Hg19::chr5:66456034..66456066,+	p@chr5:66456034..66456066 +
Hg19::chr5:80037077..80037109,+	p@chr5:80037077..80037109 +
Hg19::chr9:92316442..92316457,+	p2@ENST00000444374

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:0030497	fatty acid elongation	0.00129518426939833
GO:0030176	integral to endoplasmic reticulum membrane	0.0179167157266769
GO:0031227	intrinsic to endoplasmic reticulum membrane	0.0179167157266769
GO:0006633	fatty acid biosynthetic process	0.0179167157266769
GO:0046394	carboxylic acid biosynthetic process	0.0179167157266769
GO:0016053	organic acid biosynthetic process	0.0179167157266769
GO:0031301	integral to organelle membrane	0.0246085011185682
GO:0031300	intrinsic to organelle membrane	0.0246085011185682
GO:0006631	fatty acid metabolic process	0.0274866883838978
GO:0016747	transferase activity, transferring groups other than amino-acyl groups	0.0319478786451587
GO:0032787	monocarboxylic acid metabolic process	0.0319478786451587
GO:0016746	transferase activity, transferring acyl groups	0.0319478786451587
GO:0008610	lipid biosynthetic process	0.0331766432084341
GO:0005789	endoplasmic reticulum membrane	0.0403234035872679
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0403234035872679
GO:0044432	endoplasmic reticulum part	0.0420934887554456

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
hematopoietic stem cell	6.39e-42	172
angioblastic mesenchymal cell	6.39e-42	172
hematopoietic cell	1.89e-38	182
hematopoietic oligopotent progenitor cell	3.32e-38	165
hematopoietic multipotent progenitor cell	3.32e-38	165
leukocyte	4.24e-35	140
lymphocyte	1.57e-34	53
common lymphoid progenitor	1.57e-34	53
lymphoid lineage restricted progenitor cell	3.85e-34	52
hematopoietic lineage restricted progenitor cell	3.18e-29	124
nongranular leukocyte	1.17e-28	119
T cell	2.23e-21	25
pro-T cell	2.23e-21	25
mature alpha-beta T cell	1.06e-18	18
alpha-beta T cell	1.06e-18	18
immature T cell	1.06e-18	18
mature T cell	1.06e-18	18
immature alpha-beta T cell	1.06e-18	18
CD8-positive, alpha-beta T cell	8.70e-13	11
lymphocyte of B lineage	1.56e-11	24
pro-B cell	1.56e-11	24
myeloid cell	8.57e-11	112
common myeloid progenitor	8.57e-11	112
B cell	1.23e-07	14
mesenchymal cell	1.85e-07	358
connective tissue cell	8.53e-07	365

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	8.86e-12	102
blood island	8.86e-12	102
hemolymphoid system	1.19e-10	112
blood	1.35e-08	15
haemolymphatic fluid	1.35e-08	15
organism substance	1.35e-08	15
hemopoietic organ	3.33e-07	7
connective tissue	6.30e-07	375

Disease

Ontology term	p-value	n
hematologic cancer	3.03e-09	51
immune system cancer	3.03e-09	51
leukemia	3.49e-07	39

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
SPI1#6688	4	4.10216175426136	0.0102780066240076	0.0381906547765586

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.