Coexpression cluster:C1153

Full id: C1153_Monocytederived_CD14_Dendritic_Macrophage_acute_spleen_lymph

Phase1 CAGE Peaks

Hg19::chr11:72983377..72983428,+	p1@P2RY6
Hg19::chr11:72983450..72983455,+	p11@P2RY6
Hg19::chr1:159796094..159796108,-	p@chr1:159796094..159796108 -
Hg19::chr1:159796534..159796545,+	p6@SLAMF8
Hg19::chr1:159796561..159796581,+	p4@SLAMF8
Hg19::chr1:159796620..159796645,+	p3@SLAMF8
Hg19::chr1:159796650..159796690,+	p1@SLAMF8

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:0045029	UDP-activated nucleotide receptor activity	0.00326730049767864
GO:0015065	uridine nucleotide receptor activity	0.00326730049767864
GO:0030321	transepithelial chloride transport	0.005808106742807
GO:0045028	purinergic nucleotide receptor activity, G-protein coupled	0.0136832824560085
GO:0001608	nucleotide receptor activity, G-protein coupled	0.0136832824560085
GO:0001614	purinergic nucleotide receptor activity	0.0136832824560085
GO:0016502	nucleotide receptor activity	0.0136832824560085
GO:0006821	chloride transport	0.0212713128400425
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0212713128400425
GO:0048015	phosphoinositide-mediated signaling	0.02804667290501
GO:0015698	inorganic anion transport	0.0484567284829324
GO:0019932	second-messenger-mediated signaling	0.0484567284829324

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
macrophage dendritic cell progenitor	8.49e-43	61
monopoietic cell	6.56e-40	59
monocyte	6.56e-40	59
monoblast	6.56e-40	59
promonocyte	6.56e-40	59
granulocyte monocyte progenitor cell	9.49e-38	67
defensive cell	4.28e-36	48
phagocyte	4.28e-36	48
myeloid lineage restricted progenitor cell	2.62e-34	66
myeloid leukocyte	5.46e-32	72
classical monocyte	8.02e-27	42
CD14-positive, CD16-negative classical monocyte	8.02e-27	42
myeloid cell	1.92e-19	108
common myeloid progenitor	1.92e-19	108
nongranular leukocyte	2.87e-18	115
hematopoietic lineage restricted progenitor cell	3.41e-18	120
leukocyte	3.30e-16	136
stuff accumulating cell	5.52e-15	87
macrophage	3.54e-12	6
hematopoietic oligopotent progenitor cell	5.71e-11	161
hematopoietic multipotent progenitor cell	5.71e-11	161
hematopoietic stem cell	1.22e-10	168
angioblastic mesenchymal cell	1.22e-10	168
hematopoietic cell	1.77e-09	177
immature conventional dendritic cell	3.68e-08	5
common dendritic progenitor	3.68e-08	5
adult endothelial progenitor cell	4.83e-07	3

Uber Anatomy

Ontology term	p-value	n
immune system	1.10e-32	93
adult organism	7.14e-32	114
bone marrow	1.12e-31	76
hematopoietic system	1.28e-28	98
blood island	1.28e-28	98
bone element	2.22e-28	82
hemolymphoid system	2.52e-27	108
skeletal element	1.12e-24	90
skeletal system	6.62e-21	100
lateral plate mesoderm	8.77e-14	203
organ	3.14e-13	503
musculoskeletal system	3.90e-10	167
neural tube	7.48e-09	56
neural rod	7.48e-09	56
future spinal cord	7.48e-09	56
neural keel	7.48e-09	56
anatomical system	9.42e-09	624
anatomical group	1.08e-08	625
multi-cellular organism	4.96e-08	656
germ layer	5.11e-08	560
germ layer / neural crest	5.11e-08	560
embryonic tissue	5.11e-08	560
presumptive structure	5.11e-08	560
germ layer / neural crest derived structure	5.11e-08	560
epiblast (generic)	5.11e-08	560
neural nucleus	7.38e-08	9
nucleus of brain	7.38e-08	9
mesoderm	7.85e-08	315
mesoderm-derived structure	7.85e-08	315
presumptive mesoderm	7.85e-08	315
embryonic structure	8.73e-08	564
regional part of nervous system	9.08e-08	53
regional part of brain	9.08e-08	53
developing anatomical structure	9.16e-08	581
embryo	3.76e-07	592

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
MAFF#23764	2	16.09010185427	0.00623834681426503	0.0275300728021223
MAX#4149	7	6.45255550900712	2.14589603858566e-06	7.76560070595454e-05
MYC#4609	7	5.2222818716094	9.4355989882785e-06	0.000250876915157031
NFKB1#4790	5	3.9200453029956	0.00303658142448461	0.0161179877714855
SMARCC1#6599	2	12.4752455198947	0.0102004731657184	0.0379877056395117

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.