Coexpression cluster:C642

Full id: C642_Whole_blood_optic_substantia_globus_corpus_thalamus

Phase1 CAGE Peaks

Hg19::chr10:111985777..111985788,+	p4@MXI1
Hg19::chr10:22825620..22825656,-	p2@PIP4K2A
Hg19::chr10:22825878..22825894,-	p5@PIP4K2A
Hg19::chr10:22830771..22830779,-	p@chr10:22830771..22830779 -
Hg19::chr10:23002092..23002110,-	p@chr10:23002092..23002110 -
Hg19::chr10:23003155..23003214,+	p@chr10:23003155..23003214 +
Hg19::chr10:23003406..23003417,-	p4@PIP4K2A
Hg19::chr10:23003436..23003459,-	p3@PIP4K2A
Hg19::chr10:23003460..23003562,-	p1@PIP4K2A
Hg19::chr12:21680866..21680902,+	p6@C12orf39
Hg19::chr14:105147464..105147523,+	p1@ENST00000540171
Hg19::chr4:90758153..90758176,-	p5@SNCA
Hg19::chr8:27468262..27468277,-	p27@CLU

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:0006629	lipid metabolic process	0.0108070060423257
GO:0006916	anti-apoptosis	0.0108070060423257
GO:0016235	aggresome	0.0108070060423257
GO:0048523	negative regulation of cellular process	0.0108070060423257
GO:0006644	phospholipid metabolic process	0.0108070060423257
GO:0048519	negative regulation of biological process	0.0108070060423257
GO:0043066	negative regulation of apoptosis	0.0108070060423257
GO:0001956	positive regulation of neurotransmitter secretion	0.0108070060423257
GO:0016309	1-phosphatidylinositol-5-phosphate 4-kinase activity	0.0108070060423257
GO:0043069	negative regulation of programmed cell death	0.0108070060423257
GO:0048169	regulation of long-term neuronal synaptic plasticity	0.0116053713801532
GO:0042416	dopamine biosynthetic process	0.0116053713801532
GO:0006643	membrane lipid metabolic process	0.0116053713801532
GO:0016234	inclusion body	0.0141251242095994
GO:0031018	endocrine pancreas development	0.0141251242095994
GO:0001963	synaptic transmission, dopaminergic	0.0154484450428978
GO:0016308	1-phosphatidylinositol-4-phosphate 5-kinase activity	0.0155330633749191
GO:0042994	cytoplasmic sequestering of transcription factor	0.0155330633749191
GO:0048168	regulation of neuronal synaptic plasticity	0.0155330633749191
GO:0031016	pancreas development	0.0155330633749191
GO:0051220	cytoplasmic sequestering of protein	0.0155330633749191
GO:0042423	catecholamine biosynthetic process	0.0155330633749191
GO:0042308	negative regulation of protein import into nucleus	0.0155330633749191
GO:0042992	negative regulation of transcription factor import into nucleus	0.0155330633749191
GO:0042417	dopamine metabolic process	0.0155330633749191
GO:0046928	regulation of neurotransmitter secretion	0.0156890392781357
GO:0046823	negative regulation of nucleocytoplasmic transport	0.0156890392781357
GO:0042127	regulation of cell proliferation	0.0158233579816069
GO:0051224	negative regulation of protein transport	0.0158233579816069
GO:0048167	regulation of synaptic plasticity	0.0182152392557906
GO:0042136	neurotransmitter biosynthetic process	0.0182152392557906
GO:0050803	regulation of synapse structure and activity	0.0184797701797707
GO:0048489	synaptic vesicle transport	0.0184797701797707
GO:0042981	regulation of apoptosis	0.0184797701797707
GO:0043067	regulation of programmed cell death	0.0184797701797707
GO:0007270	nerve-nerve synaptic transmission	0.0184797701797707
GO:0042221	response to chemical stimulus	0.0184797701797707
GO:0042990	regulation of transcription factor import into nucleus	0.0184797701797707
GO:0042991	transcription factor import into nucleus	0.0184797701797707
GO:0042306	regulation of protein import into nucleus	0.0184797701797707
GO:0033157	regulation of intracellular protein transport	0.0184797701797707
GO:0016307	phosphatidylinositol phosphate kinase activity	0.0184797701797707
GO:0032507	maintenance of cellular protein localization	0.0191052624903955
GO:0051651	maintenance of cellular localization	0.0191052624903955
GO:0046488	phosphatidylinositol metabolic process	0.0191052624903955
GO:0032386	regulation of intracellular transport	0.0191052624903955
GO:0045185	maintenance of protein localization	0.0191052624903955
GO:0006584	catecholamine metabolic process	0.0191052624903955
GO:0018958	phenol metabolic process	0.0192959568263883
GO:0051223	regulation of protein transport	0.0192959568263883
GO:0006958	complement activation, classical pathway	0.0192959568263883
GO:0007399	nervous system development	0.0192959568263883
GO:0046822	regulation of nucleocytoplasmic transport	0.0192959568263883
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.0195905268674936
GO:0051051	negative regulation of transport	0.0196979209913166
GO:0008283	cell proliferation	0.0196979209913166
GO:0042133	neurotransmitter metabolic process	0.0197944119925687
GO:0035270	endocrine system development	0.0198421677209551
GO:0044255	cellular lipid metabolic process	0.0198421677209551
GO:0042401	biogenic amine biosynthetic process	0.0199776320823133
GO:0019717	synaptosome	0.0208035701289321
GO:0001727	lipid kinase activity	0.0214492439905879
GO:0006956	complement activation	0.0214492439905879
GO:0002541	activation of plasma proteins during acute inflammatory response	0.0214492439905879
GO:0007269	neurotransmitter secretion	0.0214492439905879
GO:0006915	apoptosis	0.0214492439905879
GO:0051235	maintenance of localization	0.0214492439905879
GO:0012501	programmed cell death	0.0214492439905879
GO:0042398	amino acid derivative biosynthetic process	0.0214492439905879
GO:0008219	cell death	0.0228610036321127
GO:0016265	death	0.0228610036321127
GO:0045597	positive regulation of cell differentiation	0.0229958414124646
GO:0016064	immunoglobulin mediated immune response	0.0245579892626077
GO:0019724	B cell mediated immunity	0.0245579892626077
GO:0016043	cellular component organization and biogenesis	0.0245579892626077
GO:0045055	regulated secretory pathway	0.0245579892626077
GO:0051046	regulation of secretion	0.0269735680637904
GO:0042493	response to drug	0.0284263292519867
GO:0048471	perinuclear region of cytoplasm	0.0285103237305022
GO:0004428	inositol or phosphatidylinositol kinase activity	0.0289770518895741
GO:0051649	establishment of cellular localization	0.0289770518895741
GO:0051094	positive regulation of developmental process	0.0290514758545434
GO:0003001	generation of a signal involved in cell-cell signaling	0.0290514758545434
GO:0051641	cellular localization	0.0290514758545434
GO:0002253	activation of immune response	0.0290514758545434
GO:0002449	lymphocyte mediated immunity	0.0290514758545434
GO:0040012	regulation of locomotion	0.0290514758545434
GO:0040011	locomotion	0.0290514758545434
GO:0006576	biogenic amine metabolic process	0.0290514758545434
GO:0006959	humoral immune response	0.0290514758545434
GO:0002250	adaptive immune response	0.0290514758545434
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0290514758545434
GO:0002443	leukocyte mediated immunity	0.029178169694758
GO:0001505	regulation of neurotransmitter levels	0.029178169694758
GO:0002526	acute inflammatory response	0.0292394509575832
GO:0030384	phosphoinositide metabolic process	0.0292994125000015
GO:0048468	cell development	0.0304863311065692
GO:0050778	positive regulation of immune response	0.0304863311065692
GO:0002684	positive regulation of immune system process	0.0305316306197012
GO:0006575	amino acid derivative metabolic process	0.0316247408588697
GO:0006606	protein import into nucleus	0.0333872700655214
GO:0050776	regulation of immune response	0.033417100397404
GO:0051170	nuclear import	0.033417100397404
GO:0002682	regulation of immune system process	0.0337672299085275
GO:0006650	glycerophospholipid metabolic process	0.0337781048632552
GO:0051240	positive regulation of multicellular organismal process	0.0347763791412003
GO:0003714	transcription corepressor activity	0.0351034490641594
GO:0002252	immune effector process	0.0354192425605005
GO:0051049	regulation of transport	0.0354192425605005
GO:0045087	innate immune response	0.0363649480858612
GO:0009309	amine biosynthetic process	0.0369227283928866
GO:0048667	neuron morphogenesis during differentiation	0.0369227283928866
GO:0006979	response to oxidative stress	0.0369227283928866
GO:0048812	neurite morphogenesis	0.0369227283928866
GO:0017038	protein import	0.0372073074498277
GO:0000904	cellular morphogenesis during differentiation	0.0380869794858592
GO:0031175	neurite development	0.0404372637687916
GO:0048731	system development	0.0412386355147545
GO:0045595	regulation of cell differentiation	0.0423856905548066
GO:0044271	nitrogen compound biosynthetic process	0.0429005750847962
GO:0048666	neuron development	0.0441884666926329
GO:0006913	nucleocytoplasmic transport	0.0441884666926329
GO:0051169	nuclear transport	0.0443931938023867
GO:0048869	cellular developmental process	0.0489034391672832
GO:0030154	cell differentiation	0.0489034391672832

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	1.42e-15	168
angioblastic mesenchymal cell	1.42e-15	168
hematopoietic oligopotent progenitor cell	2.57e-15	161
hematopoietic multipotent progenitor cell	2.57e-15	161
hematopoietic cell	2.65e-13	177
leukocyte	8.21e-13	136
myeloid cell	8.88e-11	108
common myeloid progenitor	8.88e-11	108
hematopoietic lineage restricted progenitor cell	1.16e-10	120
nongranular leukocyte	2.46e-10	115
myeloid leukocyte	7.47e-08	72
myeloid lineage restricted progenitor cell	7.65e-07	66

Uber Anatomy

Ontology term	p-value	n
adult organism	2.54e-35	114
neural tube	1.24e-28	56
neural rod	1.24e-28	56
future spinal cord	1.24e-28	56
neural keel	1.24e-28	56
regional part of nervous system	3.22e-26	53
regional part of brain	3.22e-26	53
brain grey matter	1.96e-23	34
gray matter	1.96e-23	34
telencephalon	2.50e-23	34
brain	1.04e-22	68
future brain	1.04e-22	68
regional part of forebrain	5.65e-22	41
forebrain	5.65e-22	41
anterior neural tube	5.65e-22	41
future forebrain	5.65e-22	41
central nervous system	6.37e-22	81
regional part of telencephalon	1.10e-21	32
cerebral hemisphere	1.46e-21	32
nervous system	4.85e-20	89
neural plate	9.17e-19	82
presumptive neural plate	9.17e-19	82
neurectoderm	6.74e-17	86
cerebral cortex	7.08e-16	25
pallium	7.08e-16	25
regional part of cerebral cortex	5.59e-15	22
pre-chordal neural plate	3.53e-14	61
neocortex	2.64e-13	20
ecto-epithelium	8.32e-12	104
hematopoietic system	1.01e-10	98
blood island	1.01e-10	98
neural nucleus	3.21e-09	9
nucleus of brain	3.21e-09	9
hemolymphoid system	4.45e-09	108
basal ganglion	5.13e-09	9
nuclear complex of neuraxis	5.13e-09	9
aggregate regional part of brain	5.13e-09	9
collection of basal ganglia	5.13e-09	9
cerebral subcortex	5.13e-09	9
blood	1.62e-08	15
haemolymphatic fluid	1.62e-08	15
organism substance	1.62e-08	15
structure with developmental contribution from neural crest	2.32e-08	132
posterior neural tube	8.02e-08	15
chordal neural plate	8.02e-08	15
telencephalic nucleus	1.81e-07	7
brainstem	9.96e-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
SRF#6722	4	4.24528561912856	0.0115903477001898	0.042349799652245

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.