Coexpression cluster:C3890

Full id: C3890_spinal_amygdala_locus_medulla_hippocampus_optic_globus

Phase1 CAGE Peaks

Hg19::chr1:160175117..160175136,+	p2@PEA15
Hg19::chr1:160175166..160175195,+	p1@PEA15
Hg19::chr1:160175201..160175212,+	p4@PEA15

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	2.81e-16	180
mesodermal cell	1.12e-11	119
fibroblast	8.57e-09	75
vascular associated smooth muscle cell	7.69e-08	32
smooth muscle cell	1.35e-07	42
smooth muscle myoblast	1.35e-07	42
contractile cell	3.18e-07	59
muscle precursor cell	3.69e-07	57
myoblast	3.69e-07	57
multi-potent skeletal muscle stem cell	3.69e-07	57
embryonic cell	7.22e-07	248

Uber Anatomy

Ontology term	p-value	n
neural tube	8.48e-29	57
neural rod	8.48e-29	57
future spinal cord	8.48e-29	57
neural keel	8.48e-29	57
central nervous system	5.73e-27	82
regional part of brain	1.73e-26	59
neural plate	8.17e-26	86
presumptive neural plate	8.17e-26	86
brain	8.50e-25	69
future brain	8.50e-25	69
tube	4.90e-24	194
regional part of nervous system	4.26e-23	94
nervous system	4.26e-23	94
cell layer	1.24e-22	312
neurectoderm	1.33e-22	90
epithelium	4.29e-22	309
anatomical conduit	1.70e-21	241
anatomical group	2.07e-21	626
anatomical system	2.89e-21	625
organism subdivision	8.66e-21	365
head	9.32e-21	123
ectoderm-derived structure	1.31e-20	169
multi-cellular organism	3.54e-20	659
anterior neural tube	5.08e-20	42
regional part of forebrain	5.66e-20	41
forebrain	5.66e-20	41
future forebrain	5.66e-20	41
gray matter	3.00e-19	34
brain grey matter	3.00e-19	34
telencephalon	4.25e-19	34
ectoderm	9.93e-19	173
presumptive ectoderm	9.93e-19	173
anatomical cluster	1.47e-18	286
regional part of telencephalon	1.55e-18	33
cerebral hemisphere	8.06e-18	32
anterior region of body	9.14e-18	129
craniocervical region	9.14e-18	129
pre-chordal neural plate	1.68e-17	61
embryonic structure	1.57e-14	605
developing anatomical structure	1.57e-14	605
germ layer	1.71e-14	604
embryonic tissue	1.71e-14	604
presumptive structure	1.71e-14	604
epiblast (generic)	1.71e-14	604
embryo	6.85e-14	612
cerebral cortex	1.52e-13	25
pallium	1.52e-13	25
splanchnic layer of lateral plate mesoderm	2.35e-12	84
organ	3.12e-12	511
regional part of cerebral cortex	3.29e-12	22
vasculature	2.28e-11	79
vascular system	2.28e-11	79
vessel	6.23e-11	69
neocortex	6.23e-11	20
organ part	1.11e-10	219
blood vessel	1.11e-10	60
epithelial tube open at both ends	1.11e-10	60
blood vasculature	1.11e-10	60
vascular cord	1.11e-10	60
artery	2.26e-10	42
arterial blood vessel	2.26e-10	42
arterial system	2.26e-10	42
posterior neural tube	5.53e-10	15
chordal neural plate	5.53e-10	15
segmental subdivision of nervous system	1.10e-08	13
multi-tissue structure	2.29e-08	347
somite	4.05e-08	83
paraxial mesoderm	4.05e-08	83
presomitic mesoderm	4.05e-08	83
presumptive segmental plate	4.05e-08	83
trunk paraxial mesoderm	4.05e-08	83
presumptive paraxial mesoderm	4.05e-08	83
adult organism	4.44e-08	115
segmental subdivision of hindbrain	4.80e-08	12
hindbrain	4.80e-08	12
presumptive hindbrain	4.80e-08	12
systemic artery	4.94e-08	33
systemic arterial system	4.94e-08	33
epithelial tube	2.27e-07	118
multilaminar epithelium	2.64e-07	82
basal ganglion	2.82e-07	9
nuclear complex of neuraxis	2.82e-07	9
aggregate regional part of brain	2.82e-07	9
collection of basal ganglia	2.82e-07	9
cerebral subcortex	2.82e-07	9
nucleus of brain	2.88e-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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325508103540109
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462515526809917
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154195629085008
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156843428463302
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276927560748377
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140284655843709

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.