Coexpression cluster:C1112

Full id: C1112_extraskeletal_corpus_Neural_thalamus_substantia_pons_medulla

Phase1 CAGE Peaks

Hg19::chr10:25304967..25304988,-	p2@ENKUR
Hg19::chr16:19612967..19612983,+	p7@C16orf62
Hg19::chr16:19896782..19896816,-	p4@GPRC5B
Hg19::chr1:66458111..66458123,+	p17@PDE4B
Hg19::chr1:66458291..66458304,+	p9@PDE4B
Hg19::chr1:66458305..66458316,+	p13@PDE4B
Hg19::chrX:43832628..43832644,-	p1@NDP

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:0007601	visual perception	0.00871228837189771
GO:0050953	sensory perception of light stimulus	0.00871228837189771
GO:0005118	sevenless binding	0.00871228837189771
GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	0.0152438119264595
GO:0001890	placenta development	0.0261230189931719
GO:0005626	insoluble fraction	0.0273585139144967
GO:0007033	vacuole organization and biogenesis	0.0273585139144967
GO:0007600	sensory perception	0.0371529700088947
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	0.0371529700088947
GO:0005102	receptor binding	0.0371529700088947
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0371529700088947
GO:0008067	metabotropic glutamate, GABA-B-like receptor activity	0.0412847974420979
GO:0050877	neurological system process	0.0452851199130761

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	6.95e-45	57
neural rod	6.95e-45	57
future spinal cord	6.95e-45	57
neural keel	6.95e-45	57
central nervous system	4.74e-41	82
regional part of nervous system	6.72e-40	94
nervous system	6.72e-40	94
regional part of brain	1.02e-37	59
adult organism	7.11e-37	115
brain	7.74e-36	69
future brain	7.74e-36	69
regional part of forebrain	8.00e-35	41
forebrain	8.00e-35	41
future forebrain	8.00e-35	41
neural plate	1.03e-33	86
presumptive neural plate	1.03e-33	86
anterior neural tube	1.67e-33	42
neurectoderm	5.24e-33	90
telencephalon	1.06e-29	34
gray matter	1.20e-29	34
brain grey matter	1.20e-29	34
regional part of telencephalon	8.38e-29	33
cerebral hemisphere	8.28e-28	32
ectoderm-derived structure	1.57e-25	169
ectoderm	1.76e-25	173
presumptive ectoderm	1.76e-25	173
pre-chordal neural plate	2.76e-24	61
anterior region of body	7.54e-23	129
craniocervical region	7.54e-23	129
head	2.45e-22	123
cerebral cortex	8.18e-22	25
pallium	8.18e-22	25
regional part of cerebral cortex	1.31e-19	22
neocortex	6.51e-18	20
embryo	2.78e-13	612
embryonic structure	6.20e-13	605
developing anatomical structure	6.20e-13	605
germ layer	1.53e-12	604
embryonic tissue	1.53e-12	604
presumptive structure	1.53e-12	604
epiblast (generic)	1.53e-12	604
posterior neural tube	3.43e-12	15
chordal neural plate	3.43e-12	15
tube	8.48e-12	194
anatomical system	1.08e-11	625
anatomical group	1.47e-11	626
multi-cellular organism	1.46e-10	659
segmental subdivision of nervous system	1.78e-10	13
organ	2.01e-10	511
anatomical conduit	2.80e-10	241
epithelium	4.74e-10	309
segmental subdivision of hindbrain	9.61e-10	12
hindbrain	9.61e-10	12
presumptive hindbrain	9.61e-10	12
cell layer	1.32e-09	312
nucleus of brain	3.05e-09	9
neural nucleus	3.05e-09	9
basal ganglion	4.05e-09	9
nuclear complex of neuraxis	4.05e-09	9
aggregate regional part of brain	4.05e-09	9
collection of basal ganglia	4.05e-09	9
cerebral subcortex	4.05e-09	9
organism subdivision	4.79e-09	365
anatomical cluster	1.20e-08	286
organ part	1.18e-07	219
temporal lobe	1.54e-07	7
telencephalic nucleus	1.66e-07	7
regional part of metencephalon	3.40e-07	9
metencephalon	3.40e-07	9
future metencephalon	3.40e-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.