Coexpression cluster:C460

Full id: C460_Neutrophils_corpus_thalamus_substantia_parietal_globus_locus

Phase1 CAGE Peaks

Hg19::chr10:1278750..1278767,-	p@chr10:1278750..1278767 -
Hg19::chr10:1282470..1282519,-	p3@ADARB2
Hg19::chr11:78049190..78049232,-	p@chr11:78049190..78049232 -
Hg19::chr2:71804278..71804331,+	p@chr2:71804278..71804331 +
Hg19::chr4:185729602..185729613,-	p15@ACSL1
Hg19::chr9:91985133..91985173,-	p@chr9:91985133..91985173 -
Hg19::chr9:91985218..91985232,-	p@chr9:91985218..91985232 -
Hg19::chr9:91985236..91985347,-	p@chr9:91985236..91985347 -
Hg19::chr9:91985398..91985439,-	p@chr9:91985398..91985439 -
Hg19::chr9:91985441..91985477,-	p@chr9:91985441..91985477 -
Hg19::chr9:91985535..91985584,-	p@chr9:91985535..91985584 -
Hg19::chr9:91985611..91985646,-	p@chr9:91985611..91985646 -
Hg19::chr9:91985687..91985700,-	p@chr9:91985687..91985700 -
Hg19::chr9:91985741..91985765,-	p@chr9:91985741..91985765 -
Hg19::chr9:91985867..91985882,-	p@chr9:91985867..91985882 -
Hg19::chr9:91985883..91985947,-	p@chr9:91985883..91985947 -
Hg19::chr9:91986315..91986327,-	p@chr9:91986315..91986327 -
Hg19::chr9:91987177..91987203,-	p@chr9:91987177..91987203 -
Hg19::chr9:91987221..91987232,-	p@chr9:91987221..91987232 -
Hg19::chr9:91987337..91987359,-	p@chr9:91987337..91987359 -
Hg19::chr9:91987399..91987413,-	p@chr9:91987399..91987413 -

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:0004467	long-chain-fatty-acid-CoA ligase activity	0.0202658856665421
GO:0015645	fatty-acid ligase activity	0.0202658856665421
GO:0004000	adenosine deaminase activity	0.0202658856665421
GO:0003727	single-stranded RNA binding	0.0202658856665421
GO:0016877	ligase activity, forming carbon-sulfur bonds	0.0202658856665421
GO:0019239	deaminase activity	0.0202658856665421
GO:0031903	microbody membrane	0.0202658856665421
GO:0005778	peroxisomal membrane	0.0202658856665421
GO:0044439	peroxisomal part	0.0202658856665421
GO:0044438	microbody part	0.0202658856665421
GO:0016814	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines	0.0202658856665421
GO:0003725	double-stranded RNA binding	0.0202658856665421
GO:0005741	mitochondrial outer membrane	0.0254740322863236
GO:0031968	organelle outer membrane	0.0254740322863236
GO:0007586	digestion	0.0254740322863236
GO:0019867	outer membrane	0.0254740322863236
GO:0042579	microbody	0.0254740322863236
GO:0005777	peroxisome	0.0254740322863236
GO:0005792	microsome	0.0387065963269252
GO:0042598	vesicular fraction	0.0387065963269252
GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	0.0397555679538304
GO:0006631	fatty acid metabolic process	0.0397555679538304

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
hematopoietic stem cell	1.36e-26	172
angioblastic mesenchymal cell	1.36e-26	172
hematopoietic oligopotent progenitor cell	7.02e-26	165
hematopoietic multipotent progenitor cell	7.02e-26	165
hematopoietic cell	6.57e-24	182
leukocyte	8.69e-24	140
nongranular leukocyte	1.91e-22	119
hematopoietic lineage restricted progenitor cell	2.95e-20	124
lymphocyte	7.30e-14	53
common lymphoid progenitor	7.30e-14	53
lymphoid lineage restricted progenitor cell	1.70e-13	52
myeloid cell	1.51e-12	112
common myeloid progenitor	1.51e-12	112
CD14-positive, CD16-negative classical monocyte	1.74e-12	42
classical monocyte	1.35e-11	45
myeloid leukocyte	2.79e-11	76
T cell	1.20e-09	25
pro-T cell	1.20e-09	25
myeloid lineage restricted progenitor cell	5.02e-09	70
monopoietic cell	1.90e-08	63
monocyte	1.90e-08	63
monoblast	1.90e-08	63
promonocyte	1.90e-08	63
mature alpha-beta T cell	1.03e-07	18
alpha-beta T cell	1.03e-07	18
immature T cell	1.03e-07	18
mature T cell	1.03e-07	18
immature alpha-beta T cell	1.03e-07	18
granulocyte monocyte progenitor cell	1.19e-07	71
macrophage dendritic cell progenitor	1.60e-07	65

Uber Anatomy

Ontology term	p-value	n
adult organism	1.90e-34	115
neural tube	7.58e-27	57
neural rod	7.58e-27	57
future spinal cord	7.58e-27	57
neural keel	7.58e-27	57
regional part of forebrain	4.59e-23	41
forebrain	4.59e-23	41
future forebrain	4.59e-23	41
central nervous system	2.16e-22	82
anterior neural tube	8.59e-22	42
regional part of brain	3.08e-20	59
regional part of nervous system	4.97e-20	94
nervous system	4.97e-20	94
brain	6.81e-20	69
future brain	6.81e-20	69
gray matter	4.12e-19	34
brain grey matter	4.12e-19	34
telencephalon	4.72e-19	34
regional part of telencephalon	1.78e-18	33
cerebral hemisphere	1.18e-17	32
neural plate	5.59e-16	86
presumptive neural plate	5.59e-16	86
neurectoderm	1.53e-15	90
regional part of cerebral cortex	6.15e-14	22
cerebral cortex	1.67e-13	25
pallium	1.67e-13	25
neocortex	1.12e-12	20
pre-chordal neural plate	3.29e-12	61
hematopoietic system	2.38e-10	102
blood island	2.38e-10	102
hemolymphoid system	1.10e-09	112
anterior region of body	3.88e-08	129
craniocervical region	3.88e-08	129
nucleus of brain	3.67e-07	9
neural nucleus	3.67e-07	9
basal ganglion	4.53e-07	9
nuclear complex of neuraxis	4.53e-07	9
aggregate regional part of brain	4.53e-07	9
collection of basal ganglia	4.53e-07	9
cerebral subcortex	4.53e-07	9
head	5.18e-07	123

Disease

Ontology term	p-value	n
hematologic cancer	1.31e-07	51
immune system cancer	1.31e-07	51

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
MYC#4609	9	2.23812080211832	0.0108503326105984	0.0400126368249105
SUZ12#23512	4	9.54586303067865	0.00072185169508612	0.00576592498532309

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.