Coexpression cluster:C3020

Full id: C3020_thymus_CD19_CD8_CD4_lymph_blood_vein

Phase1 CAGE Peaks

Hg19::chr10:47640768..47640792,-	p1@ENST00000454837
Hg19::chr1:160616854..160616893,+	p@chr1:160616854..160616893 +
Hg19::chr5:118604403..118604434,+	p4@TNFAIP8

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:0019987	negative regulation of anti-apoptosis	0.0024726245143059
GO:0043027	caspase inhibitor activity	0.0024726245143059
GO:0045767	regulation of anti-apoptosis	0.0032968326857412
GO:0043028	caspase regulator activity	0.00432709290003532
GO:0006916	anti-apoptosis	0.0270811256328741
GO:0043066	negative regulation of apoptosis	0.0270811256328741
GO:0043069	negative regulation of programmed cell death	0.0270811256328741
GO:0004857	enzyme inhibitor activity	0.0413134345931944
GO:0042981	regulation of apoptosis	0.0474743906746733
GO:0043067	regulation of programmed cell death	0.0474743906746733

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
lymphocyte	1.14e-54	53
common lymphoid progenitor	1.14e-54	53
lymphoid lineage restricted progenitor cell	2.03e-53	52
nucleate cell	3.73e-52	55
nongranular leukocyte	8.42e-31	115
leukocyte	1.33e-29	136
mature alpha-beta T cell	1.18e-26	18
alpha-beta T cell	1.18e-26	18
immature T cell	1.18e-26	18
mature T cell	1.18e-26	18
immature alpha-beta T cell	1.18e-26	18
hematopoietic lineage restricted progenitor cell	5.80e-26	120
hematopoietic stem cell	1.08e-25	168
angioblastic mesenchymal cell	1.08e-25	168
T cell	4.86e-25	25
pro-T cell	4.86e-25	25
lymphocyte of B lineage	1.06e-24	24
pro-B cell	1.06e-24	24
hematopoietic cell	1.82e-23	177
hematopoietic oligopotent progenitor cell	5.95e-23	161
hematopoietic multipotent progenitor cell	5.95e-23	161
B cell	2.07e-20	14
CD8-positive, alpha-beta T cell	1.82e-19	11
CD4-positive, alpha-beta T cell	1.07e-10	6

Uber Anatomy

Ontology term	p-value	n
blood	5.49e-15	15
haemolymphatic fluid	5.49e-15	15
organism substance	5.49e-15	15
hemopoietic organ	2.01e-09	7
immune organ	2.01e-09	7

Disease

Ontology term	p-value	n
lymphoma	4.46e-07	10

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	3	8.20432350852273	0.00181059318941052	0.0108788713674402

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.