Coexpression cluster:C317

Full id: C317_Neutrophils_medial_amygdala_occipital_hippocampus_brain_parietal

Phase1 CAGE Peaks

Hg19::chr10:12872736..12872766,+	p@chr10:12872736..12872766 +
Hg19::chr10:28872321..28872338,+	p@chr10:28872321..28872338 +
Hg19::chr17:8063613..8063632,-	p19@VAMP2
Hg19::chr17:8063633..8063652,-	p13@VAMP2
Hg19::chr17:8063773..8063784,-	p17@VAMP2
Hg19::chr17:8063896..8063935,-	p5@VAMP2
Hg19::chr17:8063940..8064027,-	p3@VAMP2
Hg19::chr17:8064030..8064075,-	p4@VAMP2
Hg19::chr17:8064076..8064105,-	p7@VAMP2
Hg19::chr17:8064108..8064167,-	p2@VAMP2
Hg19::chr17:8064820..8064846,-	p@chr17:8064820..8064846 -
Hg19::chr17:8064981..8064994,-	p@chr17:8064981..8064994 -
Hg19::chr17:8065006..8065022,-	p@chr17:8065006..8065022 -
Hg19::chr17:8065032..8065092,-	p@chr17:8065032..8065092 -
Hg19::chr17:8065618..8065647,-	p6@VAMP2
Hg19::chr19:21476394..21476407,-	p5@ZNF708
Hg19::chr1:182352898..182352944,-	p@chr1:182352898..182352944 -
Hg19::chr22:22162032..22162049,-	p@chr22:22162032..22162049 -
Hg19::chr22:22221658..22221669,-	p2@MAPK1
Hg19::chr2:55252842..55252854,-	p37@RTN4
Hg19::chr2:55253582..55253618,-	p21@RTN4
Hg19::chr4:146296807..146296819,+	p2@RTN3P1
Hg19::chr5:108714170..108714199,-	p@chr5:108714170..108714199 -
Hg19::chr5:108714529..108714568,-	p@chr5:108714529..108714568 -
Hg19::chr5:108717346..108717361,-	p@chr5:108717346..108717361 -
Hg19::chr7:135614485..135614494,-	p@chr7:135614485..135614494 -
Hg19::chrX:148561290..148561301,-	p@chrX:148561290..148561301 -
Hg19::chrX:148561796..148561820,-	p7@IDS
Hg19::chrX:148562594..148562662,-	p9@IDS
Hg19::chrX:148562710..148562819,-	p5@IDS
Hg19::chrX:148563677..148563702,-	p15@IDS
Hg19::chrX:148564109..148564137,-	p@chrX:148564109..148564137 -
Hg19::chrX:148564140..148564173,-	p@chrX:148564140..148564173 -
Hg19::chrX:148564210..148564228,-	p@chrX:148564210..148564228 -
Hg19::chrX:148568487..148568517,-	p@chrX:148568487..148568517 -
Hg19::chrX:148579666..148579690,-	p12@IDS
Hg19::chrX:17095433..17095443,+	p@chrX:17095433..17095443 +

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:0051093	negative regulation of developmental process	0.011056054917044
GO:0004423	iduronate-2-sulfatase activity	0.0148286915920051
GO:0019858	cytosine metabolic process	0.0148286915920051
GO:0019987	negative regulation of anti-apoptosis	0.0148286915920051
GO:0043330	response to exogenous dsRNA	0.0148286915920051
GO:0030517	negative regulation of axon extension	0.0148286915920051
GO:0050793	regulation of developmental process	0.0148286915920051
GO:0032496	response to lipopolysaccharide	0.014872125970684
GO:0031663	lipopolysaccharide-mediated signaling pathway	0.014872125970684
GO:0001784	phosphotyrosine binding	0.014872125970684
GO:0045309	protein phosphorylated amino acid binding	0.014872125970684
GO:0043331	response to dsRNA	0.014872125970684
GO:0050771	negative regulation of axonogenesis	0.014872125970684
GO:0002237	response to molecule of bacterial origin	0.0214743725119483
GO:0051219	phosphoprotein binding	0.0214743725119483
GO:0050768	negative regulation of neurogenesis	0.0214743725119483
GO:0045767	regulation of anti-apoptosis	0.0214743725119483
GO:0030516	regulation of axon extension	0.0214743725119483
GO:0006206	pyrimidine base metabolic process	0.0220381900309618
GO:0048675	axon extension	0.027371766138232
GO:0042981	regulation of apoptosis	0.0276148747912329
GO:0043067	regulation of programmed cell death	0.0276148747912329
GO:0043229	intracellular organelle	0.0291760839094347
GO:0043226	organelle	0.0291760839094347
GO:0009112	nucleobase metabolic process	0.0296154479966804
GO:0050770	regulation of axonogenesis	0.0321850191184355
GO:0008484	sulfuric ester hydrolase activity	0.0381317353245734
GO:0004707	MAP kinase activity	0.0390634055895234
GO:0019717	synaptosome	0.0399303007690236
GO:0050767	regulation of neurogenesis	0.0407388984608223
GO:0006915	apoptosis	0.0418259096100216
GO:0012501	programmed cell death	0.0418259096100216
GO:0008219	cell death	0.0435619786122206
GO:0016265	death	0.0435619786122206
GO:0030203	glycosaminoglycan metabolic process	0.0446382964742239
GO:0006022	aminoglycan metabolic process	0.0446382964742239
GO:0030176	integral to endoplasmic reticulum membrane	0.0460296366314013
GO:0044424	intracellular part	0.0465090500924841
GO:0030334	regulation of cell migration	0.0477864562370677
GO:0009653	anatomical structure morphogenesis	0.0477864562370677
GO:0031227	intrinsic to endoplasmic reticulum membrane	0.0477864562370677
GO:0045596	negative regulation of cell differentiation	0.0493315820358417
GO:0005737	cytoplasm	0.0493315820358417
GO:0051270	regulation of cell motility	0.0498513608352335
GO:0048523	negative regulation of cellular process	0.0498513608352335
GO:0040012	regulation of locomotion	0.0498513608352335
GO:0040011	locomotion	0.0498513608352335

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
neural tube	2.95e-34	56
neural rod	2.95e-34	56
future spinal cord	2.95e-34	56
neural keel	2.95e-34	56
central nervous system	1.18e-33	81
adult organism	3.77e-33	114
nervous system	3.65e-32	89
regional part of nervous system	5.18e-32	53
regional part of brain	5.18e-32	53
brain	3.89e-30	68
future brain	3.89e-30	68
regional part of forebrain	2.65e-28	41
forebrain	2.65e-28	41
anterior neural tube	2.65e-28	41
future forebrain	2.65e-28	41
neurectoderm	8.21e-24	86
brain grey matter	9.64e-24	34
gray matter	9.64e-24	34
telencephalon	1.61e-23	34
neural plate	2.36e-23	82
presumptive neural plate	2.36e-23	82
cerebral hemisphere	2.72e-22	32
regional part of telencephalon	3.05e-22	32
regional part of cerebral cortex	6.94e-18	22
pre-chordal neural plate	2.73e-17	61
cerebral cortex	5.18e-17	25
pallium	5.18e-17	25
neocortex	3.46e-16	20
ectoderm-derived structure	2.05e-14	171
ectoderm	2.05e-14	171
presumptive ectoderm	2.05e-14	171
ecto-epithelium	6.62e-14	104
structure with developmental contribution from neural crest	7.12e-14	132
organ system subdivision	2.18e-12	223
basal ganglion	1.84e-08	9
nuclear complex of neuraxis	1.84e-08	9
aggregate regional part of brain	1.84e-08	9
collection of basal ganglia	1.84e-08	9
cerebral subcortex	1.84e-08	9
neural nucleus	3.16e-08	9
nucleus of brain	3.16e-08	9
posterior neural tube	2.42e-07	15
chordal neural plate	2.42e-07	15
telencephalic nucleus	9.25e-07	7

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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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.