Coexpression cluster:C1954

Full id: C1954_occipital_parietal_temporal_duodenum_brain_Neurons_medulloblastoma

Phase1 CAGE Peaks

Hg19::chr5:146833190..146833201,-	p10@DPYSL3
Hg19::chr5:146833206..146833217,-	p9@DPYSL3
Hg19::chr5:146833222..146833261,-	p1@DPYSL3
Hg19::chr5:146833451..146833484,-	p5@DPYSL3
Hg19::chr5:146833803..146833825,-	p14@DPYSL3

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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No GOStat results

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	7.31e-14	180
neural cell	8.29e-10	25
vascular associated smooth muscle cell	3.31e-09	32
electrically responsive cell	5.74e-09	60
electrically active cell	5.74e-09	60
neurectodermal cell	8.59e-09	59
smooth muscle cell	6.76e-08	42
smooth muscle myoblast	6.76e-08	42

Uber Anatomy

Ontology term	p-value	n
central nervous system	3.92e-28	82
regional part of nervous system	1.71e-27	94
nervous system	1.71e-27	94
multi-cellular organism	5.97e-26	659
tube	1.07e-24	194
neural plate	3.38e-24	86
presumptive neural plate	3.38e-24	86
ectoderm-derived structure	5.72e-24	169
anatomical conduit	3.35e-23	241
ectoderm	1.95e-22	173
presumptive ectoderm	1.95e-22	173
embryo	3.78e-22	612
neurectoderm	7.96e-22	90
anatomical cluster	9.46e-22	286
brain	9.35e-21	69
future brain	9.35e-21	69
epithelium	1.11e-20	309
anatomical group	1.73e-20	626
cell layer	2.64e-20	312
anatomical system	3.66e-20	625
neural tube	4.01e-20	57
neural rod	4.01e-20	57
future spinal cord	4.01e-20	57
neural keel	4.01e-20	57
embryonic structure	1.17e-18	605
developing anatomical structure	1.17e-18	605
germ layer	3.06e-18	604
embryonic tissue	3.06e-18	604
presumptive structure	3.06e-18	604
epiblast (generic)	3.06e-18	604
adult organism	3.57e-18	115
regional part of brain	4.14e-18	59
head	2.11e-17	123
anterior region of body	2.11e-16	129
craniocervical region	2.11e-16	129
organism subdivision	9.64e-16	365
splanchnic layer of lateral plate mesoderm	1.10e-15	84
pre-chordal neural plate	1.21e-15	61
multi-tissue structure	4.52e-15	347
anterior neural tube	2.30e-14	42
regional part of forebrain	2.89e-14	41
forebrain	2.89e-14	41
future forebrain	2.89e-14	41
gray matter	2.44e-13	34
brain grey matter	2.44e-13	34
telencephalon	4.89e-13	34
regional part of telencephalon	8.64e-13	33
cerebral hemisphere	3.18e-12	32
blood vessel	3.85e-12	60
epithelial tube open at both ends	3.85e-12	60
blood vasculature	3.85e-12	60
vascular cord	3.85e-12	60
vasculature	5.17e-12	79
vascular system	5.17e-12	79
artery	5.85e-12	42
arterial blood vessel	5.85e-12	42
arterial system	5.85e-12	42
organ	9.30e-11	511
epithelial tube	1.00e-10	118
organ part	1.05e-10	219
vessel	1.69e-10	69
cerebral cortex	9.35e-10	25
pallium	9.35e-10	25
systemic artery	2.46e-09	33
systemic arterial system	2.46e-09	33
circulatory system	7.49e-09	113
cardiovascular system	9.56e-09	110
regional part of cerebral cortex	3.35e-08	22
heart	1.92e-07	24
primitive heart tube	1.92e-07	24
primary heart field	1.92e-07	24
anterior lateral plate mesoderm	1.92e-07	24
heart tube	1.92e-07	24
heart primordium	1.92e-07	24
cardiac mesoderm	1.92e-07	24
cardiogenic plate	1.92e-07	24
heart rudiment	1.92e-07	24
muscle tissue	2.27e-07	63
musculature	2.27e-07	63
musculature of body	2.27e-07	63
neocortex	2.61e-07	20
primary circulatory organ	2.84e-07	27
posterior neural tube	4.62e-07	15
chordal neural plate	4.62e-07	15
skeletal muscle tissue	6.98e-07	61
striated muscle tissue	6.98e-07	61
myotome	6.98e-07	61

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
CTCF#10664	5	5.36025637307503	0.000225927829993709	0.00250192732867277
EGR1#1958	4	3.99054327584811	0.006780098300144	0.0287754667737621
RAD21#5885	5	10.3550338954563	8.39503550283973e-06	0.000229881781038563
SMC3#9126	5	15.0449328449328	1.29633924985553e-06	5.16749522578862e-05
YY1#7528	5	4.91117074985386	0.0003499314082136	0.00353106148235943
ZNF143#7702	3	8.10052593133674	0.00362487051209098	0.0183366197526044

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.