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	6.13e-15	250
mesodermal cell	1.21e-13	121
non-terminally differentiated cell	1.91e-12	106
contractile cell	2.44e-12	59
electrically responsive cell	2.99e-12	61
electrically active cell	2.99e-12	61
smooth muscle cell	4.38e-12	43
smooth muscle myoblast	4.38e-12	43
vascular associated smooth muscle cell	6.85e-12	32
muscle precursor cell	7.03e-12	58
myoblast	7.03e-12	58
multi-potent skeletal muscle stem cell	7.03e-12	58
muscle cell	1.09e-11	55

Uber Anatomy

Ontology term	p-value	n
cell layer	1.70e-30	309
epithelium	9.98e-30	306
central nervous system	1.02e-29	81
nervous system	4.49e-29	89
brain	1.11e-27	68
future brain	1.11e-27	68
tube	2.35e-27	192
neural tube	3.22e-24	56
neural rod	3.22e-24	56
future spinal cord	3.22e-24	56
neural keel	3.22e-24	56
ectoderm-derived structure	6.43e-24	171
ectoderm	6.43e-24	171
presumptive ectoderm	6.43e-24	171
anatomical cluster	1.56e-23	373
neural plate	1.61e-23	82
presumptive neural plate	1.61e-23	82
regional part of nervous system	2.13e-23	53
regional part of brain	2.13e-23	53
neurectoderm	8.24e-23	86
structure with developmental contribution from neural crest	1.60e-22	132
anatomical conduit	2.20e-22	240
ecto-epithelium	1.18e-21	104
pre-chordal neural plate	1.00e-18	61
regional part of forebrain	1.47e-18	41
forebrain	1.47e-18	41
anterior neural tube	1.47e-18	41
future forebrain	1.47e-18	41
brain grey matter	5.92e-17	34
gray matter	5.92e-17	34
cerebral hemisphere	6.68e-17	32
telencephalon	2.04e-16	34
regional part of telencephalon	6.16e-16	32
multi-tissue structure	7.34e-16	342
vasculature	1.31e-14	78
vascular system	1.31e-14	78
cerebral cortex	7.40e-14	25
pallium	7.40e-14	25
regional part of cerebral cortex	1.19e-13	22
artery	1.19e-12	42
arterial blood vessel	1.19e-12	42
arterial system	1.19e-12	42
neocortex	1.25e-12	20
splanchnic layer of lateral plate mesoderm	1.81e-12	83
epithelial tube open at both ends	3.50e-12	59
blood vessel	3.50e-12	59
blood vasculature	3.50e-12	59
vascular cord	3.50e-12	59
vessel	1.37e-11	68
skeletal muscle tissue	1.08e-10	62
striated muscle tissue	1.08e-10	62
myotome	1.08e-10	62
systemic artery	1.72e-10	33
systemic arterial system	1.72e-10	33
circulatory system	2.33e-10	112
multilaminar epithelium	4.84e-10	83
muscle tissue	6.26e-10	64
musculature	6.26e-10	64
musculature of body	6.26e-10	64
cardiovascular system	7.29e-10	109
epithelial vesicle	8.63e-10	78
paraxial mesoderm	1.50e-09	72
presumptive paraxial mesoderm	1.50e-09	72
dense mesenchyme tissue	1.50e-09	73
epithelial tube	2.76e-09	117
multi-cellular organism	2.95e-09	656
somite	4.02e-09	71
presomitic mesoderm	4.02e-09	71
presumptive segmental plate	4.02e-09	71
dermomyotome	4.02e-09	71
trunk paraxial mesoderm	4.02e-09	71
anatomical system	4.42e-09	624
organ part	4.51e-09	218
anatomical group	6.09e-09	625
embryo	1.56e-08	592
developing anatomical structure	2.05e-08	581
organ system subdivision	4.13e-08	223
embryonic structure	1.68e-07	564
posterior neural tube	6.97e-07	15
chordal neural plate	6.97e-07	15
germ layer	8.47e-07	560
germ layer / neural crest	8.47e-07	560
embryonic tissue	8.47e-07	560
presumptive structure	8.47e-07	560
germ layer / neural crest derived structure	8.47e-07	560
epiblast (generic)	8.47e-07	560

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.