Coexpression cluster:C4250

Full id: C4250_Macrophage_CD14_lung_Monocytederived_Melanocyte_Dendritic_mature

Phase1 CAGE Peaks

Hg19::chr2:86110452..86110460,+	p@chr2:86110452..86110460 +
Hg19::chr3:15382885..15382889,-	p2@SH3BP5
Hg19::chr5:36680383..36680394,+	p15@SLC1A3

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:0005313	L-glutamate transmembrane transporter activity	0.00900529667184184
GO:0001504	neurotransmitter uptake	0.00900529667184184
GO:0015172	acidic amino acid transmembrane transporter activity	0.00900529667184184
GO:0015813	L-glutamate transport	0.00900529667184184
GO:0015800	acidic amino acid transport	0.00900529667184184
GO:0017153	sodium:dicarboxylate symporter activity	0.00900529667184184
GO:0005310	dicarboxylic acid transmembrane transporter activity	0.00900529667184184
GO:0006835	dicarboxylic acid transport	0.00900529667184184
GO:0015179	L-amino acid transmembrane transporter activity	0.013686271723284
GO:0005343	organic acid:sodium symporter activity	0.013686271723284
GO:0015296	anion:cation symporter activity	0.013686271723284
GO:0004860	protein kinase inhibitor activity	0.013686271723284
GO:0019210	kinase inhibitor activity	0.013686271723284
GO:0005070	SH3/SH2 adaptor activity	0.0148252658539005
GO:0060090	molecular adaptor activity	0.0161167081592623
GO:0015171	amino acid transmembrane transporter activity	0.0161167081592623
GO:0006865	amino acid transport	0.0161167081592623
GO:0006836	neurotransmitter transport	0.0161167081592623
GO:0001505	regulation of neurotransmitter levels	0.0161167081592623
GO:0015837	amine transport	0.0161167081592623
GO:0015370	solute:sodium symporter activity	0.0161167081592623
GO:0030674	protein binding, bridging	0.0161167081592623
GO:0046943	carboxylic acid transmembrane transporter activity	0.0161167081592623
GO:0046942	carboxylic acid transport	0.0161167081592623
GO:0015849	organic acid transport	0.0161167081592623
GO:0005342	organic acid transmembrane transporter activity	0.0161167081592623
GO:0019887	protein kinase regulator activity	0.0164589308333072
GO:0015294	solute:cation symporter activity	0.0172292068078032
GO:0019207	kinase regulator activity	0.0178003717136349
GO:0008509	anion transmembrane transporter activity	0.0294397965576245
GO:0015293	symporter activity	0.0329724945737631
GO:0007268	synaptic transmission	0.0382505891715711
GO:0019226	transmission of nerve impulse	0.0421825913579477
GO:0015291	secondary active transmembrane transporter activity	0.0446441028060174
GO:0004857	enzyme inhibitor activity	0.0482784473309191

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
granulocyte monocyte progenitor cell	2.62e-51	71
macrophage dendritic cell progenitor	5.07e-50	65
myeloid lineage restricted progenitor cell	7.79e-50	70
monopoietic cell	1.62e-49	63
monocyte	1.62e-49	63
monoblast	1.62e-49	63
promonocyte	1.62e-49	63
myeloid leukocyte	7.20e-47	76
CD14-positive, CD16-negative classical monocyte	3.94e-40	42
classical monocyte	9.18e-37	45
myeloid cell	1.19e-28	112
common myeloid progenitor	1.19e-28	112
hematopoietic lineage restricted progenitor cell	4.73e-27	124
nongranular leukocyte	8.86e-25	119
leukocyte	1.68e-24	140
hematopoietic oligopotent progenitor cell	1.20e-17	165
hematopoietic multipotent progenitor cell	1.20e-17	165
hematopoietic stem cell	3.43e-17	172
angioblastic mesenchymal cell	3.43e-17	172
hematopoietic cell	1.85e-15	182
macrophage	2.58e-07	10
adult endothelial progenitor cell	7.12e-07	3

Uber Anatomy

Ontology term	p-value	n
bone marrow	6.45e-44	80
bone element	7.53e-40	86
hemolymphoid system	1.40e-39	112
hematopoietic system	1.63e-39	102
blood island	1.63e-39	102
immune system	1.32e-36	115
skeletal element	8.32e-32	101
skeletal system	8.32e-32	101
musculoskeletal system	1.08e-14	167
lateral plate mesoderm	1.25e-13	216

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.