Coexpression cluster:C2525

Full id: C2525_neuroblastoma_nonsmall_Neurons_Neural_temporal_duodenum_brain

Phase1 CAGE Peaks

Hg19::chr1:151032739..151032748,+	p6@MLLT11
Hg19::chr1:151032782..151032801,+	p4@MLLT11
Hg19::chr1:151032833..151032850,+	p3@MLLT11
Hg19::chr1:151032860..151032918,+	p1@MLLT11

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
embryonic cell	1.23e-15	248
mesodermal cell	1.28e-13	119
non-terminally differentiated cell	3.08e-13	180
electrically responsive cell	5.37e-13	60
electrically active cell	5.37e-13	60
contractile cell	9.33e-13	59
smooth muscle cell	1.71e-12	42
smooth muscle myoblast	1.71e-12	42
vascular associated smooth muscle cell	5.32e-12	32
muscle precursor cell	7.76e-12	57
myoblast	7.76e-12	57
multi-potent skeletal muscle stem cell	7.76e-12	57
muscle cell	1.11e-11	54
ectodermal cell	4.73e-08	71

Uber Anatomy

Ontology term	p-value	n
central nervous system	2.47e-30	82
cell layer	3.06e-30	312
regional part of nervous system	6.76e-30	94
nervous system	6.76e-30	94
epithelium	2.35e-29	309
brain	6.12e-27	69
future brain	6.12e-27	69
tube	5.51e-26	194
ectoderm-derived structure	1.08e-24	169
ectoderm	2.15e-24	173
presumptive ectoderm	2.15e-24	173
neural plate	2.67e-24	86
presumptive neural plate	2.67e-24	86
regional part of brain	1.27e-23	59
neurectoderm	1.53e-23	90
neural tube	4.54e-23	57
neural rod	4.54e-23	57
future spinal cord	4.54e-23	57
neural keel	4.54e-23	57
head	3.58e-22	123
anatomical conduit	2.79e-20	241
anterior region of body	3.52e-20	129
craniocervical region	3.52e-20	129
organism subdivision	5.95e-20	365
regional part of forebrain	1.55e-18	41
forebrain	1.55e-18	41
future forebrain	1.55e-18	41
pre-chordal neural plate	1.72e-18	61
anterior neural tube	2.83e-17	42
gray matter	3.24e-17	34
brain grey matter	3.24e-17	34
cerebral hemisphere	3.33e-17	32
telencephalon	1.06e-16	34
regional part of telencephalon	4.75e-16	33
anatomical cluster	1.07e-15	286
vasculature	3.92e-15	79
vascular system	3.92e-15	79
cerebral cortex	2.37e-14	25
pallium	2.37e-14	25
regional part of cerebral cortex	7.96e-14	22
multi-tissue structure	3.52e-13	347
neocortex	8.10e-13	20
blood vessel	1.54e-12	60
epithelial tube open at both ends	1.54e-12	60
blood vasculature	1.54e-12	60
vascular cord	1.54e-12	60
splanchnic layer of lateral plate mesoderm	2.04e-12	84
artery	2.27e-12	42
arterial blood vessel	2.27e-12	42
arterial system	2.27e-12	42
vessel	1.29e-11	69
circulatory system	2.61e-11	113
cardiovascular system	9.26e-11	110
skeletal muscle tissue	1.26e-10	61
striated muscle tissue	1.26e-10	61
myotome	1.26e-10	61
systemic artery	4.19e-10	33
systemic arterial system	4.19e-10	33
muscle tissue	6.17e-10	63
musculature	6.17e-10	63
musculature of body	6.17e-10	63
somite	7.89e-10	83
paraxial mesoderm	7.89e-10	83
presomitic mesoderm	7.89e-10	83
presumptive segmental plate	7.89e-10	83
trunk paraxial mesoderm	7.89e-10	83
presumptive paraxial mesoderm	7.89e-10	83
multilaminar epithelium	9.97e-10	82
organ part	2.32e-09	219
dermomyotome	6.21e-09	70
epithelial tube	9.78e-09	118
multi-cellular organism	2.48e-07	659
embryo	2.76e-07	612
posterior neural tube	5.16e-07	15
chordal neural plate	5.16e-07	15
anatomical system	5.45e-07	625
anatomical group	8.26e-07	626
germ layer	8.71e-07	604
embryonic tissue	8.71e-07	604
presumptive structure	8.71e-07	604
epiblast (generic)	8.71e-07	604
embryonic structure	8.79e-07	605
developing anatomical structure	8.79e-07	605

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
CTBP2#1488	4	62.7170003393281	6.45042639894877e-08	3.95814384653238e-06
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101467957682995
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160935195341284
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00434449754964212
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186135630045954
MAFK#7975	4	27.1007331378299	1.85228494563408e-06	6.85266693011258e-05
REST#5978	4	9.65002871612802	0.000115282561421917	0.00157077565979695
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00796622629481037
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00684466027270313
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322346995279321
TBP#6908	4	3.70677068709639	0.00529637781478435	0.02443127081835
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00508089318284221
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106890507322528
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00346668130899418

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.