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><br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	1.11e-09	168
angioblastic mesenchymal cell	1.11e-09	168
leukocyte	2.08e-09	136
hematopoietic cell	8.46e-09	177
nongranular leukocyte	1.23e-08	115
hematopoietic oligopotent progenitor cell	1.35e-08	161
hematopoietic multipotent progenitor cell	1.35e-08	161
lymphocyte	1.09e-07	53
common lymphoid progenitor	1.09e-07	53
lymphoid lineage restricted progenitor cell	3.56e-07	52
nucleate cell	3.71e-07	55
hematopoietic lineage restricted progenitor cell	7.71e-07	120

Uber Anatomy

Ontology term	p-value	n
neural tube	1.05e-43	56
neural rod	1.05e-43	56
future spinal cord	1.05e-43	56
neural keel	1.05e-43	56
regional part of nervous system	2.74e-40	53
regional part of brain	2.74e-40	53
adult organism	7.31e-36	114
regional part of forebrain	1.09e-35	41
forebrain	1.09e-35	41
anterior neural tube	1.09e-35	41
future forebrain	1.09e-35	41
brain	7.83e-34	68
future brain	7.83e-34	68
central nervous system	7.68e-33	81
nervous system	2.27e-31	89
neural plate	3.19e-29	82
presumptive neural plate	3.19e-29	82
brain grey matter	3.19e-28	34
gray matter	3.19e-28	34
telencephalon	3.54e-28	34
neurectoderm	3.59e-28	86
regional part of telencephalon	7.04e-26	32
cerebral hemisphere	1.11e-25	32
pre-chordal neural plate	1.79e-23	61
regional part of cerebral cortex	1.30e-21	22
neocortex	2.10e-19	20
ecto-epithelium	3.43e-19	104
cerebral cortex	3.34e-18	25
pallium	3.34e-18	25
structure with developmental contribution from neural crest	5.59e-15	132
basal ganglion	5.87e-12	9
nuclear complex of neuraxis	5.87e-12	9
aggregate regional part of brain	5.87e-12	9
collection of basal ganglia	5.87e-12	9
cerebral subcortex	5.87e-12	9
neural nucleus	6.49e-12	9
nucleus of brain	6.49e-12	9
ectoderm-derived structure	2.56e-10	171
ectoderm	2.56e-10	171
presumptive ectoderm	2.56e-10	171
telencephalic nucleus	1.55e-09	7
posterior neural tube	2.89e-09	15
chordal neural plate	2.89e-09	15
diencephalon	5.38e-09	7
future diencephalon	5.38e-09	7
brainstem	1.02e-08	6
organ system subdivision	1.43e-08	223
gyrus	4.26e-08	6
limbic system	2.03e-07	5
segmental subdivision of nervous system	2.53e-07	13
parietal lobe	4.60e-07	5
temporal lobe	9.55e-07	6

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.