Coexpression cluster:C842

Full id: C842_Neutrophils_CD14CD16_CD14_Eosinophils_migratory_Mesenchymal_Fibroblast

Phase1 CAGE Peaks

Hg19::chr16:84600281..84600315,-	p@chr16:84600281..84600315 -
Hg19::chr16:84600344..84600356,-	p@chr16:84600344..84600356 -
Hg19::chr16:84600375..84600405,-	p@chr16:84600375..84600405 -
Hg19::chr16:84600432..84600461,-	p@chr16:84600432..84600461 -
Hg19::chr16:84600468..84600488,-	p@chr16:84600468..84600488 -
Hg19::chr16:84623794..84623816,-	p3@COTL1
Hg19::chr16:84623843..84623875,-	p4@COTL1
Hg19::chr16:84651647..84651667,-	p2@COTL1
Hg19::chr16:84651673..84651691,-	p1@COTL1
Hg19::chr3:50294928..50294962,+	p1@AY555145

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:0031280	negative regulation of cyclase activity	0.0155978685153231
GO:0007194	negative regulation of adenylate cyclase activity	0.0155978685153231
GO:0051350	negative regulation of lyase activity	0.0155978685153231
GO:0045761	regulation of adenylate cyclase activity	0.0187100024153625
GO:0007584	response to nutrient	0.0187100024153625
GO:0031279	regulation of cyclase activity	0.0187100024153625
GO:0051339	regulation of lyase activity	0.0187100024153625
GO:0031667	response to nutrient levels	0.0225929366485817
GO:0009991	response to extracellular stimulus	0.0225929366485817
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0225929366485817
GO:0019933	cAMP-mediated signaling	0.0225929366485817
GO:0043086	negative regulation of catalytic activity	0.0225929366485817
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0271420350435088
GO:0019935	cyclic-nucleotide-mediated signaling	0.0271420350435088

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
somatic cell	1.50e-32	591
native cell	9.24e-29	722
animal cell	4.88e-27	679
eukaryotic cell	4.88e-27	679
CD14-positive, CD16-negative classical monocyte	1.12e-26	42
myeloid leukocyte	1.07e-25	76
classical monocyte	1.39e-24	45
multi fate stem cell	1.74e-23	430
monopoietic cell	1.81e-23	63
monocyte	1.81e-23	63
monoblast	1.81e-23	63
promonocyte	1.81e-23	63
somatic stem cell	5.10e-23	436
macrophage dendritic cell progenitor	9.32e-22	65
stem cell	1.07e-21	444
myeloid lineage restricted progenitor cell	1.35e-19	70
granulocyte monocyte progenitor cell	2.38e-19	71
mesodermal cell	5.39e-17	119
leukocyte	2.36e-14	140
connective tissue cell	3.11e-13	365
myeloid cell	3.79e-13	112
common myeloid progenitor	3.79e-13	112
nongranular leukocyte	4.31e-13	119
mesenchymal cell	2.12e-12	358
contractile cell	1.92e-11	59
muscle precursor cell	1.75e-10	57
myoblast	1.75e-10	57
multi-potent skeletal muscle stem cell	1.75e-10	57
muscle cell	3.03e-10	54
hematopoietic lineage restricted progenitor cell	4.44e-10	124
smooth muscle cell	1.41e-09	42
smooth muscle myoblast	1.41e-09	42
electrically responsive cell	1.53e-09	60
electrically active cell	1.53e-09	60
motile cell	3.08e-09	390
hematopoietic oligopotent progenitor cell	1.97e-08	165
hematopoietic multipotent progenitor cell	1.97e-08	165
vascular associated smooth muscle cell	4.03e-08	32
hematopoietic stem cell	6.95e-08	172
angioblastic mesenchymal cell	6.95e-08	172
hematopoietic cell	1.81e-07	182
lining cell	2.86e-07	57
barrier cell	2.86e-07	57
non-terminally differentiated cell	3.30e-07	180
embryonic cell	6.08e-07	248

Uber Anatomy

Ontology term	p-value	n
musculoskeletal system	5.51e-22	167
lateral plate mesoderm	2.80e-21	216
hemolymphoid system	2.42e-18	112
bone marrow	2.38e-17	80
hematopoietic system	4.49e-17	102
blood island	4.49e-17	102
bone element	2.17e-14	86
skeletal element	5.81e-14	101
skeletal system	5.81e-14	101
connective tissue	2.11e-11	375
immune system	3.00e-11	115
dermomyotome	6.13e-10	70
mesoderm	6.55e-10	448
mesoderm-derived structure	6.55e-10	448
presumptive mesoderm	6.55e-10	448
somite	8.32e-10	83
paraxial mesoderm	8.32e-10	83
presomitic mesoderm	8.32e-10	83
presumptive segmental plate	8.32e-10	83
trunk paraxial mesoderm	8.32e-10	83
presumptive paraxial mesoderm	8.32e-10	83
multilaminar epithelium	1.33e-09	82
cardiovascular system	2.93e-09	110
vasculature	1.90e-08	79
vascular system	1.90e-08	79
skeletal muscle tissue	4.57e-08	61
striated muscle tissue	4.57e-08	61
myotome	4.57e-08	61
circulatory system	5.14e-08	113
muscle tissue	2.53e-07	63
musculature	2.53e-07	63
musculature of body	2.53e-07	63
artery	2.53e-07	42
arterial blood vessel	2.53e-07	42
arterial system	2.53e-07	42
vessel	5.74e-07	69

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
SP1#6667	7	3.98886696469863	0.000373436559150151	0.00371193878377107

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.