Coexpression cluster:C808

Full id: C808_Neural_spinal_cerebral_hippocampus_cerebellum_duodenum_corpus

Phase1 CAGE Peaks

Hg19::chr11:82444874..82444886,-	p2@FAM181B
Hg19::chr11:82444929..82444940,-	p4@FAM181B
Hg19::chr3:147657764..147657816,+	p1@ENST00000467198 p1@ENST00000485006 p1@uc003ewf.1
Hg19::chr6:30848740..30848768,+	p8@DDR1
Hg19::chr6:30848771..30848818,+	p7@DDR1
Hg19::chr7:136936091..136936115,-	p@chr7:136936091..136936115 -
Hg19::chr7:137028434..137028487,-	p2@PTN
Hg19::chr7:137028498..137028519,-	p6@PTN
Hg19::chr7:137028534..137028548,-	p3@PTN
Hg19::chrX:70389721..70389757,+	p@chrX:70389721..70389757 +

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:0007167	enzyme linked receptor protein signaling pathway	0.00777254054695249
GO:0007185	transmembrane receptor protein tyrosine phosphatase signaling pathway	0.0176603039176693
GO:0007612	learning	0.0294277743350421
GO:0030282	bone mineralization	0.0294277743350421
GO:0004864	protein phosphatase inhibitor activity	0.0343248214812073
GO:0019212	phosphatase inhibitor activity	0.0343248214812073
GO:0007611	learning and/or memory	0.0369818444756987
GO:0008201	heparin binding	0.0373143987937461
GO:0019888	protein phosphatase regulator activity	0.0373143987937461
GO:0019208	phosphatase regulator activity	0.0373143987937461
GO:0007166	cell surface receptor linked signal transduction	0.0373143987937461
GO:0031214	biomineral formation	0.0373143987937461
GO:0001503	ossification	0.0373143987937461
GO:0046849	bone remodeling	0.0373143987937461
GO:0048771	tissue remodeling	0.0373143987937461
GO:0004714	transmembrane receptor protein tyrosine kinase activity	0.0373143987937461
GO:0005539	glycosaminoglycan binding	0.0373143987937461
GO:0030247	polysaccharide binding	0.0373143987937461
GO:0001871	pattern binding	0.0373143987937461
GO:0019199	transmembrane receptor protein kinase activity	0.0373143987937461

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	6.78e-08	180

Uber Anatomy

Ontology term	p-value	n
central nervous system	2.57e-44	82
regional part of nervous system	7.62e-44	94
nervous system	7.62e-44	94
ectoderm-derived structure	1.14e-37	169
ectoderm	1.30e-37	173
presumptive ectoderm	1.30e-37	173
neural tube	8.33e-37	57
neural rod	8.33e-37	57
future spinal cord	8.33e-37	57
neural keel	8.33e-37	57
brain	4.04e-36	69
future brain	4.04e-36	69
regional part of brain	1.63e-35	59
neural plate	3.78e-35	86
presumptive neural plate	3.78e-35	86
adult organism	5.17e-35	115
head	6.04e-35	123
anterior region of body	1.41e-34	129
craniocervical region	1.41e-34	129
neurectoderm	1.51e-34	90
anterior neural tube	1.99e-27	42
regional part of forebrain	4.28e-27	41
forebrain	4.28e-27	41
future forebrain	4.28e-27	41
pre-chordal neural plate	4.84e-25	61
organism subdivision	2.64e-23	365
telencephalon	8.70e-23	34
gray matter	8.81e-23	34
brain grey matter	8.81e-23	34
regional part of telencephalon	3.45e-22	33
cerebral hemisphere	2.31e-21	32
multi-tissue structure	3.83e-20	347
cerebral cortex	5.30e-17	25
pallium	5.30e-17	25
regional part of cerebral cortex	2.81e-15	22
multi-cellular organism	3.02e-15	659
neocortex	5.01e-14	20
organ	9.21e-14	511
cell layer	3.18e-13	312
organ part	8.24e-13	219
epithelium	1.73e-12	309
embryo	3.13e-12	612
anatomical cluster	5.01e-12	286
anatomical system	1.36e-11	625
anatomical conduit	1.53e-11	241
anatomical group	2.30e-11	626
posterior neural tube	2.39e-10	15
chordal neural plate	2.39e-10	15
tube	2.76e-10	194
embryonic structure	5.40e-10	605
developing anatomical structure	5.40e-10	605
germ layer	1.08e-09	604
embryonic tissue	1.08e-09	604
presumptive structure	1.08e-09	604
epiblast (generic)	1.08e-09	604
segmental subdivision of nervous system	5.46e-09	13
segmental subdivision of hindbrain	2.44e-08	12
hindbrain	2.44e-08	12
presumptive hindbrain	2.44e-08	12
basal ganglion	3.12e-07	9
nuclear complex of neuraxis	3.12e-07	9
aggregate regional part of brain	3.12e-07	9
collection of basal ganglia	3.12e-07	9
cerebral subcortex	3.12e-07	9
nucleus of brain	3.14e-07	9
neural nucleus	3.14e-07	9

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.