Coexpression cluster:C256

Full id: C256_occipital_caudate_amygdala_medial_thalamus_hippocampus_medulla

Phase1 CAGE Peaks

Hg19::chr10:83635586..83635597,+	p6@NRG3
Hg19::chr11:10529999..10530000,-	p3@MIR4485
Hg19::chr12:48111295..48111297,-	p@chr12:48111295..48111297 -
Hg19::chr12:53438340..53438344,+	p@chr12:53438340..53438344 +
Hg19::chr13:110775905..110775918,+	p1@LOC283485
Hg19::chr14:101313715..101313726,-	p3@AK126659
Hg19::chr14:101314924..101314935,-	p@chr14:101314924..101314935 -
Hg19::chr14:102551227..102551242,+	p@chr14:102551227..102551242 +
Hg19::chr14:73570140..73570193,-	p@chr14:73570140..73570193 -
Hg19::chr15:34260460..34260472,+	p2@CHRM5
Hg19::chr15:34260686..34260710,+	p1@CHRM5
Hg19::chr15:69019611..69019647,+	p@chr15:69019611..69019647 +
Hg19::chr16:68750222..68750228,+	p@chr16:68750222..68750228 +
Hg19::chr17:22023159..22023161,+	p@chr17:22023159..22023161 +
Hg19::chr18:32400519..32400523,-	p@chr18:32400519..32400523 -
Hg19::chr19:45298867..45298869,+	p@chr19:45298867..45298869 +
Hg19::chr1:204580692..204580695,-	p@chr1:204580692..204580695 -
Hg19::chr1:24645071..24645074,+	p@chr1:24645071..24645074 +
Hg19::chr22:49283073..49283079,+	p@chr22:49283073..49283079 +
Hg19::chr2:165410518..165410520,+	p@chr2:165410518..165410520 +
Hg19::chr2:220348295..220348300,+	p@chr2:220348295..220348300 +
Hg19::chr2:70951535..70951538,+	p@chr2:70951535..70951538 +
Hg19::chr3:14873451..14873452,+	p@chr3:14873451..14873452 +
Hg19::chr3:88650202..88650205,+	p1@ENST00000468361
Hg19::chr4:88415555..88415573,+	p@chr4:88415555..88415573 +
Hg19::chr4:88447806..88447810,+	p@chr4:88447806..88447810 +
Hg19::chr5:134259812..134259816,+	p3@MTND6P4
Hg19::chr5:134260393..134260413,+	p@chr5:134260393..134260413 +
Hg19::chr5:134263450..134263463,+	p2@MIR4461
Hg19::chr5:134263476..134263487,+	p6@MIR4461
Hg19::chr6:121756901..121756912,+	p4@GJA1
Hg19::chr6:2911513..2911514,+	p@chr6:2911513..2911514 +
Hg19::chr7:103179905..103179918,-	p4@RELN
Hg19::chr7:105516839..105516841,+	p10@CDHR3
Hg19::chr8:104184270..104184280,-	p2@ENST00000521102
Hg19::chr8:131961464..131961485,+	p@chr8:131961464..131961485 +
Hg19::chr8:24774826..24774901,-	p@chr8:24774826..24774901 -
Hg19::chr8:24775032..24775050,-	p@chr8:24775032..24775050 -
Hg19::chr8:24775054..24775104,-	p@chr8:24775054..24775104 -
Hg19::chr8:24775187..24775201,-	p@chr8:24775187..24775201 -
Hg19::chr8:24775491..24775536,-	p@chr8:24775491..24775536 -
Hg19::chr8:24810309..24810339,+	p2@CU691685
Hg19::chr9:2157655..2157669,+	p24@SMARCA2
Hg19::chrM:1604..1614,+	p1@uc004cor.1
Hg19::chrM:5322..5344,-	p6@AK000561
Hg19::chrM:5715..5730,-	p11@AK000561
Hg19::chrX:101380689..101380700,+	p4@TCEAL2
Hg19::chrX:102632720..102632761,+	p8@NGFRAP1
Hg19::chrX:138724994..138725023,-	p2@MCF2
Hg19::chrX:20135072..20135077,-	p9@MAP7D2
Hg19::chrX:46618069..46618072,+	p@chrX:46618069..46618072 +

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:0032989	cellular structure morphogenesis	0.000399668203536365
GO:0000902	cell morphogenesis	0.000399668203536365
GO:0031175	neurite development	0.000399668203536365
GO:0048666	neuron development	0.000445259638768424
GO:0032990	cell part morphogenesis	0.000563980050971357
GO:0048858	cell projection morphogenesis	0.000563980050971357
GO:0030030	cell projection organization and biogenesis	0.000563980050971357
GO:0030182	neuron differentiation	0.000563980050971357
GO:0048699	generation of neurons	0.000765924806671898
GO:0022008	neurogenesis	0.000873649736739441
GO:0001764	neuron migration	0.00091837531401086
GO:0007242	intracellular signaling cascade	0.00091837531401086
GO:0032501	multicellular organismal process	0.00125855994145845
GO:0009653	anatomical structure morphogenesis	0.00143788039807146
GO:0007275	multicellular organismal development	0.00157067795046963
GO:0048468	cell development	0.00244710526549635
GO:0010232	vascular transport	0.00490369231408565
GO:0048731	system development	0.00533642506746418
GO:0048667	neuron morphogenesis during differentiation	0.00533642506746418
GO:0048812	neurite morphogenesis	0.00533642506746418
GO:0000904	cellular morphogenesis during differentiation	0.00533642506746418
GO:0032502	developmental process	0.00533642506746418
GO:0050794	regulation of cellular process	0.00533642506746418
GO:0016264	gap junction assembly	0.00533642506746418
GO:0015867	ATP transport	0.00533642506746418
GO:0051503	adenine nucleotide transport	0.00533642506746418
GO:0015865	purine nucleotide transport	0.00533642506746418
GO:0045844	positive regulation of striated muscle development	0.00533642506746418
GO:0007197	muscarinic acetylcholine receptor, adenylate cyclase inhibiting pathway	0.00533642506746418
GO:0048869	cellular developmental process	0.00533642506746418
GO:0030154	cell differentiation	0.00533642506746418
GO:0007399	nervous system development	0.00533642506746418
GO:0009966	regulation of signal transduction	0.0067577507656406
GO:0050789	regulation of biological process	0.0067577507656406
GO:0048856	anatomical structure development	0.0067577507656406
GO:0006862	nucleotide transport	0.0067577507656406
GO:0030297	transmembrane receptor protein tyrosine kinase activator activity	0.0067577507656406
GO:0015872	dopamine transport	0.00793685771538271
GO:0005771	multivesicular body	0.00793685771538271
GO:0043403	skeletal muscle regeneration	0.00793685771538271
GO:0002070	epithelial cell maturation	0.00793685771538271
GO:0030971	receptor tyrosine kinase binding	0.00793685771538271
GO:0065007	biological regulation	0.00850290002631808
GO:0048265	response to pain	0.00850290002631808
GO:0005916	fascia adherens	0.00850290002631808
GO:0002064	epithelial cell development	0.00850290002631808
GO:0005243	gap junction channel activity	0.00850290002631808
GO:0045732	positive regulation of protein catabolic process	0.00850290002631808
GO:0021511	spinal cord patterning	0.00850290002631808
GO:0016477	cell migration	0.00900988650186093
GO:0009790	embryonic development	0.00900988650186093
GO:0022829	wide pore channel activity	0.00943243420928138
GO:0030296	protein tyrosine kinase activator activity	0.00943243420928138
GO:0035050	embryonic heart tube development	0.010231206359391
GO:0007512	adult heart development	0.010231206359391
GO:0007213	acetylcholine receptor signaling, muscarinic pathway	0.010231206359391
GO:0009896	positive regulation of catabolic process	0.010231206359391
GO:0048513	organ development	0.0109249402049422
GO:0009268	response to pH	0.0109249402049422
GO:0051057	positive regulation of small GTPase mediated signal transduction	0.0109249402049422
GO:0004981	muscarinic acetylcholine receptor activity	0.0109249402049422
GO:0001947	heart looping	0.01209107719632
GO:0021510	spinal cord development	0.0132199216909085
GO:0033555	multicellular organismal response to stress	0.014913734021112
GO:0051924	regulation of calcium ion transport	0.014913734021112
GO:0016358	dendrite development	0.014913734021112
GO:0030295	protein kinase activator activity	0.014913734021112
GO:0005887	integral to plasma membrane	0.0150330141389711
GO:0007165	signal transduction	0.0150330141389711
GO:0031226	intrinsic to plasma membrane	0.0150330141389711
GO:0005913	cell-cell adherens junction	0.0150330141389711
GO:0016202	regulation of striated muscle development	0.0150330141389711
GO:0007243	protein kinase cascade	0.01554022287202
GO:0007043	intercellular junction assembly	0.01554022287202
GO:0030879	mammary gland development	0.01554022287202
GO:0006928	cell motility	0.0156024026347067
GO:0051674	localization of cell	0.0156024026347067
GO:0003007	heart morphogenesis	0.0168575278318891
GO:0042246	tissue regeneration	0.0168575278318891
GO:0043269	regulation of ion transport	0.0172516267171345
GO:0042176	regulation of protein catabolic process	0.0172516267171345
GO:0045216	intercellular junction assembly and maintenance	0.0172516267171345
GO:0007193	G-protein signaling, adenylate cyclase inhibiting pathway	0.0172516267171345
GO:0031099	regeneration	0.0172516267171345
GO:0019209	kinase activator activity	0.0172516267171345
GO:0030054	cell junction	0.0172516267171345
GO:0007154	cell communication	0.0172516267171345
GO:0016043	cellular component organization and biogenesis	0.0176900902268137
GO:0030165	PDZ domain binding	0.0184888344915059
GO:0017124	SH3 domain binding	0.0184888344915059
GO:0015464	acetylcholine receptor activity	0.0191979659125002
GO:0051056	regulation of small GTPase mediated signal transduction	0.0196776083318331
GO:0042166	acetylcholine binding	0.0196776083318331
GO:0007028	cytoplasm organization and biogenesis	0.021233740315628
GO:0009894	regulation of catabolic process	0.0218833993021424
GO:0005922	connexon complex	0.0242466077980364
GO:0010001	glial cell differentiation	0.0248511060954488
GO:0005921	gap junction	0.0288236293168925
GO:0042063	gliogenesis	0.029902594608196
GO:0030855	epithelial cell differentiation	0.029902594608196
GO:0048589	developmental growth	0.030425799462554
GO:0007267	cell-cell signaling	0.0319381431203324
GO:0018108	peptidyl-tyrosine phosphorylation	0.0335238577028587
GO:0008016	regulation of heart contraction	0.0335238577028587
GO:0018212	peptidyl-tyrosine modification	0.0342602000701058
GO:0043176	amine binding	0.0342602000701058
GO:0004434	inositol or phosphatidylinositol phosphodiesterase activity	0.0342602000701058
GO:0048469	cell maturation	0.0342602000701058
GO:0004435	phosphoinositide phospholipase C activity	0.0342602000701058
GO:0048732	gland development	0.0345091178567572
GO:0003015	heart process	0.0345091178567572
GO:0014704	intercalated disc	0.0345091178567572
GO:0060047	heart contraction	0.0345091178567572
GO:0005769	early endosome	0.0356546550359624
GO:0001701	in utero embryonic development	0.036062220017993
GO:0005770	late endosome	0.036462611212125
GO:0008283	cell proliferation	0.0372426018765522
GO:0021700	developmental maturation	0.0372426018765522
GO:0005912	adherens junction	0.037622550838198
GO:0007411	axon guidance	0.0385236784114739
GO:0044459	plasma membrane part	0.0385236784114739
GO:0004629	phospholipase C activity	0.0387241888721976
GO:0051259	protein oligomerization	0.0417571008387655
GO:0002009	morphogenesis of an epithelium	0.0420840877689062
GO:0008227	amine receptor activity	0.0443797674482315
GO:0006915	apoptosis	0.0450017594557596
GO:0012501	programmed cell death	0.0453442917401657
GO:0007264	small GTPase mediated signal transduction	0.0461864129273724
GO:0016265	death	0.0488876038405213
GO:0008219	cell death	0.0488876038405213
GO:0006836	neurotransmitter transport	0.0492438315404021

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
regional part of nervous system	2.39e-128	53
regional part of brain	2.39e-128	53
neural tube	5.44e-128	56
neural rod	5.44e-128	56
future spinal cord	5.44e-128	56
neural keel	5.44e-128	56
brain	8.31e-103	68
future brain	8.31e-103	68
regional part of forebrain	7.51e-97	41
forebrain	7.51e-97	41
anterior neural tube	7.51e-97	41
future forebrain	7.51e-97	41
central nervous system	2.45e-90	81
brain grey matter	9.27e-88	34
gray matter	9.27e-88	34
telencephalon	3.68e-87	34
cerebral hemisphere	7.92e-86	32
neural plate	1.31e-85	82
presumptive neural plate	1.31e-85	82
neurectoderm	2.46e-81	86
nervous system	8.88e-81	89
regional part of telencephalon	5.38e-79	32
ecto-epithelium	3.99e-66	104
regional part of cerebral cortex	6.90e-64	22
adult organism	8.34e-64	114
pre-chordal neural plate	1.66e-63	61
cerebral cortex	4.90e-56	25
pallium	4.90e-56	25
neocortex	5.34e-55	20
structure with developmental contribution from neural crest	1.35e-53	132
ectoderm-derived structure	3.50e-39	171
ectoderm	3.50e-39	171
presumptive ectoderm	3.50e-39	171
neural nucleus	1.13e-33	9
nucleus of brain	1.13e-33	9
basal ganglion	1.18e-33	9
nuclear complex of neuraxis	1.18e-33	9
aggregate regional part of brain	1.18e-33	9
collection of basal ganglia	1.18e-33	9
cerebral subcortex	1.18e-33	9
tube	1.50e-32	192
segmental subdivision of hindbrain	7.20e-31	12
hindbrain	7.20e-31	12
presumptive hindbrain	7.20e-31	12
posterior neural tube	2.86e-30	15
chordal neural plate	2.86e-30	15
organ system subdivision	4.81e-30	223
gyrus	8.14e-29	6
segmental subdivision of nervous system	2.24e-28	13
brainstem	3.45e-28	6
telencephalic nucleus	1.12e-24	7
anatomical conduit	1.52e-24	240
limbic system	2.10e-24	5
corpus striatum	6.88e-20	4
striatum	6.88e-20	4
ventral part of telencephalon	6.88e-20	4
future corpus striatum	6.88e-20	4
regional part of metencephalon	8.50e-19	9
metencephalon	8.50e-19	9
future metencephalon	8.50e-19	9
organ part	2.27e-18	218
epithelium	1.32e-17	306
cell layer	2.32e-17	309
temporal lobe	3.05e-17	6
caudate-putamen	1.14e-15	3
dorsal striatum	1.14e-15	3
parietal lobe	2.06e-15	5
frontal cortex	2.63e-15	3
pons	5.17e-15	3
anatomical cluster	5.39e-15	373
medulla oblongata	5.98e-15	3
myelencephalon	5.98e-15	3
future myelencephalon	5.98e-15	3
multi-tissue structure	7.27e-15	342
regional part of diencephalon	1.19e-11	4
diencephalon	2.31e-11	7
future diencephalon	2.31e-11	7
middle frontal gyrus	4.27e-11	2
Ammon's horn	4.72e-11	2
lobe parts of cerebral cortex	4.72e-11	2
hippocampal formation	4.72e-11	2
limbic lobe	4.72e-11	2
caudate nucleus	4.96e-11	2
future caudate nucleus	4.96e-11	2
middle temporal gyrus	5.75e-11	2
locus ceruleus	6.67e-11	2
brainstem nucleus	6.67e-11	2
hindbrain nucleus	6.67e-11	2
amygdala	7.01e-11	2
dorsal plus ventral thalamus	9.41e-11	2
globus pallidus	9.41e-11	2
pallidum	9.41e-11	2
thalamic complex	9.41e-11	2
occipital lobe	2.12e-09	5
organ	2.75e-08	503
cerebellum	7.66e-08	6
rhombic lip	7.66e-08	6
germ layer	2.55e-07	560
germ layer / neural crest	2.55e-07	560
embryonic tissue	2.55e-07	560

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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