Coexpression cluster:C361

Full id: C361_Neural_Astrocyte_Neurons_spinal_Chondrocyte_Fibroblast_sacrococcigeal

Phase1 CAGE Peaks

Hg19::chr11:33912780..33912786,-	p@chr11:33912780..33912786 -
Hg19::chr12:106976837..106976850,+	p5@RFX4
Hg19::chr12:56075553..56075558,+	p5@METTL7B
Hg19::chr14:29236460..29236467,+	p12@FOXG1
Hg19::chr14:51562037..51562053,-	p2@TRIM9
Hg19::chr17:61228693..61228707,+	p@chr17:61228693..61228707 +
Hg19::chr19:19356203..19356221,+	p@chr19:19356203..19356221 +
Hg19::chr1:205306210..205306228,-	p@chr1:205306210..205306228 -
Hg19::chr1:205325850..205325870,-	p2@KLHDC8A
Hg19::chr1:23696308..23696339,-	p2@ZNF436
Hg19::chr1:23696348..23696363,-	p4@ZNF436
Hg19::chr20:20472232..20472244,-	p@chr20:20472232..20472244 -
Hg19::chr21:34186006..34186019,-	p2@C21orf62
Hg19::chr2:210288885..210288888,+	p33@MAP2
Hg19::chr3:62228762..62228795,+	p6@PTPRG
Hg19::chr3:62228807..62228819,+	p10@PTPRG
Hg19::chr3:78719376..78719409,-	p8@ROBO1
Hg19::chr3:78719410..78719451,-	p5@ROBO1
Hg19::chr3:78719667..78719679,-	p17@ROBO1
Hg19::chr4:48545900..48545919,-	p@chr4:48545900..48545919 -
Hg19::chr4:48545952..48545965,-	p@chr4:48545952..48545965 -
Hg19::chr5:140857085..140857104,+	p@chr5:140857085..140857104 +
Hg19::chr5:63510296..63510308,+	p@chr5:63510296..63510308 +
Hg19::chr7:121513374..121513415,+	p5@PTPRZ1
Hg19::chr7:121513478..121513517,+	p4@PTPRZ1
Hg19::chr7:121513532..121513545,+	p6@PTPRZ1
Hg19::chr7:137028222..137028235,-	p7@PTN
Hg19::chr7:137028246..137028346,-	p1@PTN
Hg19::chr7:137028364..137028380,-	p4@PTN
Hg19::chr7:137028392..137028410,-	p5@PTN
Hg19::chr9:126774091..126774098,+	p4@LHX2

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:0007399	nervous system development	0.000557336611267514
GO:0019198	transmembrane receptor protein phosphatase activity	0.00126058469449034
GO:0005001	transmembrane receptor protein tyrosine phosphatase activity	0.00126058469449034
GO:0007417	central nervous system development	0.00332990684368422
GO:0004089	carbonate dehydratase activity	0.00416377714289835
GO:0048731	system development	0.00453165753797798
GO:0048856	anatomical structure development	0.0109183876950834
GO:0016836	hydro-lyase activity	0.0109183876950834
GO:0016835	carbon-oxygen lyase activity	0.012211174528187
GO:0007275	multicellular organismal development	0.0145106528423907
GO:0008046	axon guidance receptor activity	0.0172644645043749
GO:0007420	brain development	0.0172644645043749
GO:0006730	one-carbon compound metabolic process	0.0197690695565447
GO:0007185	transmembrane receptor protein tyrosine phosphatase signaling pathway	0.0273903705317438
GO:0050789	regulation of biological process	0.0273903705317438
GO:0004725	protein tyrosine phosphatase activity	0.0314416979328173
GO:0006470	protein amino acid dephosphorylation	0.037793969519023
GO:0065007	biological regulation	0.0387732940610384
GO:0032502	developmental process	0.0387732940610384
GO:0016829	lyase activity	0.0387732940610384
GO:0016311	dephosphorylation	0.0387732940610384
GO:0050772	positive regulation of axonogenesis	0.0387732940610384
GO:0007610	behavior	0.0387732940610384
GO:0007167	enzyme linked receptor protein signaling pathway	0.0387732940610384
GO:0009888	tissue development	0.0387732940610384
GO:0004721	phosphoprotein phosphatase activity	0.0392051887455054
GO:0050769	positive regulation of neurogenesis	0.0405101214388895
GO:0007612	learning	0.0414980733231299
GO:0048513	organ development	0.0442590823351491
GO:0030282	bone mineralization	0.0442590823351491
GO:0032501	multicellular organismal process	0.0442590823351491
GO:0007026	negative regulation of microtubule depolymerization	0.0442590823351491
GO:0031114	regulation of microtubule depolymerization	0.0442590823351491
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.0442590823351491
GO:0007019	microtubule depolymerization	0.0442590823351491
GO:0050794	regulation of cellular process	0.0442590823351491
GO:0050770	regulation of axonogenesis	0.0460191143005335
GO:0009953	dorsal/ventral pattern formation	0.0460191143005335
GO:0016791	phosphoric monoester hydrolase activity	0.0460191143005335
GO:0005887	integral to plasma membrane	0.0460191143005335
GO:0031110	regulation of microtubule polymerization or depolymerization	0.0460191143005335
GO:0019222	regulation of metabolic process	0.0460191143005335
GO:0008270	zinc ion binding	0.0460191143005335
GO:0031226	intrinsic to plasma membrane	0.0460191143005335
GO:0031109	microtubule polymerization or depolymerization	0.0484864686669324
GO:0004864	protein phosphatase inhibitor activity	0.0489067669941368

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
non-terminally differentiated cell	1.99e-14	180
neural cell	1.61e-07	25

Uber Anatomy

Ontology term	p-value	n
central nervous system	2.86e-43	82
regional part of nervous system	5.13e-41	94
nervous system	5.13e-41	94
brain	5.71e-36	69
future brain	5.71e-36	69
neural tube	1.07e-34	57
neural rod	1.07e-34	57
future spinal cord	1.07e-34	57
neural keel	1.07e-34	57
ectoderm-derived structure	2.30e-34	169
head	1.60e-33	123
ectoderm	1.71e-33	173
presumptive ectoderm	1.71e-33	173
neural plate	1.97e-33	86
presumptive neural plate	1.97e-33	86
regional part of brain	5.25e-33	59
anterior region of body	1.03e-32	129
craniocervical region	1.03e-32	129
neurectoderm	8.47e-32	90
organism subdivision	3.94e-29	365
adult organism	2.93e-28	115
anterior neural tube	3.57e-26	42
regional part of forebrain	4.27e-26	41
forebrain	4.27e-26	41
future forebrain	4.27e-26	41
pre-chordal neural plate	1.07e-23	61
telencephalon	4.54e-22	34
gray matter	5.55e-22	34
brain grey matter	5.55e-22	34
regional part of telencephalon	1.90e-21	33
cerebral hemisphere	5.12e-21	32
multi-tissue structure	3.14e-19	347
multi-cellular organism	1.19e-18	659
cell layer	1.09e-17	312
cerebral cortex	6.07e-17	25
pallium	6.07e-17	25
epithelium	7.57e-17	309
anatomical cluster	1.39e-16	286
anatomical conduit	1.80e-16	241
anatomical system	1.92e-15	625
anatomical group	3.58e-15	626
tube	4.95e-15	194
regional part of cerebral cortex	5.85e-15	22
neocortex	1.04e-13	20
embryo	1.92e-13	612
organ	3.72e-13	511
embryonic structure	1.66e-11	605
developing anatomical structure	1.66e-11	605
germ layer	3.38e-11	604
embryonic tissue	3.38e-11	604
presumptive structure	3.38e-11	604
epiblast (generic)	3.38e-11	604
organ part	1.68e-10	219
posterior neural tube	1.52e-09	15
chordal neural plate	1.52e-09	15
segmental subdivision of nervous system	4.28e-08	13
segmental subdivision of hindbrain	9.95e-08	12
hindbrain	9.95e-08	12
presumptive hindbrain	9.95e-08	12

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.