Coexpression cluster:C3094

Full id: C3094_rectum_small_colon_Eosinophils_temporal_appendix_CD4

Phase1 CAGE Peaks

Hg19::chr11:119056158..119056172,+	p2@PDZD3
Hg19::chr1:2488426..2488475,-	p1@LOC100133445 p1@LOC115110
Hg19::chr1:2488477..2488501,-	p1@ENST00000452793

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:0030824	negative regulation of cGMP metabolic process	0.000392480081635857
GO:0030823	regulation of cGMP metabolic process	0.000392480081635857
GO:0035003	subapical complex	0.000392480081635857
GO:0030826	regulation of cGMP biosynthetic process	0.000392480081635857
GO:0030827	negative regulation of cGMP biosynthetic process	0.000392480081635857
GO:0030251	guanylate cyclase inhibitor activity	0.000392480081635857
GO:0019934	cGMP-mediated signaling	0.00067282299709004
GO:0030803	negative regulation of cyclic nucleotide biosynthetic process	0.000706464146944542
GO:0030800	negative regulation of cyclic nucleotide metabolic process	0.000706464146944542
GO:0030809	negative regulation of nucleotide biosynthetic process	0.000706464146944542
GO:0007168	receptor guanylyl cyclase signaling pathway	0.00100923449563506
GO:0030802	regulation of cyclic nucleotide biosynthetic process	0.00100923449563506
GO:0045980	negative regulation of nucleotide metabolic process	0.00100923449563506
GO:0030808	regulation of nucleotide biosynthetic process	0.00100923449563506
GO:0030799	regulation of cyclic nucleotide metabolic process	0.00103026021429412
GO:0030249	guanylate cyclase regulator activity	0.00103026021429412
GO:0006140	regulation of nucleotide metabolic process	0.00112624719078115
GO:0008200	ion channel inhibitor activity	0.00112624719078115
GO:0016248	channel inhibitor activity	0.00112624719078115
GO:0046068	cGMP metabolic process	0.00112624719078115
GO:0006182	cGMP biosynthetic process	0.00112624719078115
GO:0006833	water transport	0.00112624719078115
GO:0042044	fluid transport	0.00112624719078115
GO:0009636	response to toxin	0.00235488048981514
GO:0016247	channel regulator activity	0.0033910279053338
GO:0009190	cyclic nucleotide biosynthetic process	0.00362289306125406
GO:0009187	cyclic nucleotide metabolic process	0.00428924660644901
GO:0009890	negative regulation of biosynthetic process	0.00428924660644901
GO:0008022	protein C-terminus binding	0.00600900538780416
GO:0045177	apical part of cell	0.00675065740413673
GO:0043296	apical junction complex	0.00772695160720593
GO:0016327	apicolateral plasma membrane	0.00772695160720593
GO:0019935	cyclic-nucleotide-mediated signaling	0.00870592181083174
GO:0005911	intercellular junction	0.0119821860217065
GO:0009889	regulation of biosynthetic process	0.0146002590368539
GO:0009165	nucleotide biosynthetic process	0.0166804034695239
GO:0019932	second-messenger-mediated signaling	0.0170569721964989
GO:0007167	enzyme linked receptor protein signaling pathway	0.0185911617616985
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0192617147756674
GO:0009117	nucleotide metabolic process	0.0200164841634287
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0210790521893209
GO:0031324	negative regulation of cellular metabolic process	0.0213621301576088
GO:0004857	enzyme inhibitor activity	0.02196062968409
GO:0030054	cell junction	0.0228161754124311
GO:0009892	negative regulation of metabolic process	0.0228161754124311
GO:0005829	cytosol	0.0290776547438044
GO:0042221	response to chemical stimulus	0.0295111618830025
GO:0005624	membrane fraction	0.0335079869696613
GO:0000267	cell fraction	0.0433490245268012

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
leukocyte	5.20e-36	140
hematopoietic lineage restricted progenitor cell	1.07e-30	124
hematopoietic stem cell	1.35e-28	172
angioblastic mesenchymal cell	1.35e-28	172
hematopoietic oligopotent progenitor cell	2.27e-27	165
hematopoietic multipotent progenitor cell	2.27e-27	165
nongranular leukocyte	2.40e-27	119
hematopoietic cell	2.22e-26	182
lymphocyte	1.57e-18	53
common lymphoid progenitor	1.57e-18	53
lymphoid lineage restricted progenitor cell	1.77e-18	52
myeloid leukocyte	1.24e-14	76
granulocyte monocyte progenitor cell	5.72e-12	71
myeloid lineage restricted progenitor cell	6.96e-12	70
myeloid cell	6.98e-11	112
common myeloid progenitor	6.98e-11	112
macrophage dendritic cell progenitor	3.44e-10	65
T cell	5.44e-10	25
pro-T cell	5.44e-10	25
monopoietic cell	2.81e-09	63
monocyte	2.81e-09	63
monoblast	2.81e-09	63
promonocyte	2.81e-09	63
mature alpha-beta T cell	4.18e-09	18
alpha-beta T cell	4.18e-09	18
immature T cell	4.18e-09	18
mature T cell	4.18e-09	18
immature alpha-beta T cell	4.18e-09	18
lymphocyte of B lineage	1.79e-08	24
pro-B cell	1.79e-08	24
CD14-positive, CD16-negative classical monocyte	2.27e-07	42
CD8-positive, alpha-beta T cell	5.62e-07	11

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	2.92e-19	112
hematopoietic system	6.21e-19	102
blood island	6.21e-19	102
immune system	1.73e-12	115
adult organism	2.84e-10	115
bone marrow	3.01e-10	80
bone element	1.86e-08	86
blood	3.40e-08	15
haemolymphatic fluid	3.40e-08	15
organism substance	3.40e-08	15

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)
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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.