Coexpression cluster:C3151

Full id: C3151_neuroblastoma_pineal_rectum_duodenum_caudate_locus_submaxillary

Phase1 CAGE Peaks

Hg19::chr11:43290911..43290922,-	p2@HNRNPKP3
Hg19::chr11:43290929..43290949,-	p1@HNRNPKP3
Hg19::chr2:113251697..113251704,+	p16@TTL

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:0030516	regulation of axon extension	0.0137613328623572
GO:0048675	axon extension	0.0137613328623572
GO:0050770	regulation of axonogenesis	0.013923230896032
GO:0050767	regulation of neurogenesis	0.013923230896032
GO:0004835	tubulin-tyrosine ligase activity	0.013923230896032
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0191579339848503
GO:0007409	axonogenesis	0.0191579339848503
GO:0048667	neuron morphogenesis during differentiation	0.0191579339848503
GO:0048812	neurite morphogenesis	0.0191579339848503
GO:0000904	cellular morphogenesis during differentiation	0.0191579339848503
GO:0031175	neurite development	0.0191579339848503
GO:0030955	potassium ion binding	0.0191579339848503
GO:0048666	neuron development	0.0191786901430137
GO:0032990	cell part morphogenesis	0.0195896620746497
GO:0030030	cell projection organization and biogenesis	0.0195896620746497
GO:0048858	cell projection morphogenesis	0.0195896620746497
GO:0030182	neuron differentiation	0.0195896620746497
GO:0031420	alkali metal ion binding	0.0195896620746497
GO:0050793	regulation of developmental process	0.0195896620746497
GO:0048699	generation of neurons	0.0195896620746497
GO:0022008	neurogenesis	0.0201987070584739
GO:0016881	acid-amino acid ligase activity	0.0220034145767102
GO:0007017	microtubule-based process	0.022172991568504
GO:0016879	ligase activity, forming carbon-nitrogen bonds	0.0250267377055614
GO:0000287	magnesium ion binding	0.0286619481839074
GO:0032989	cellular structure morphogenesis	0.0286619481839074
GO:0000902	cell morphogenesis	0.0286619481839074
GO:0016874	ligase activity	0.0374100099241392
GO:0007010	cytoskeleton organization and biogenesis	0.0382972590003126
GO:0007399	nervous system development	0.0386396640370501

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	2.81e-67	57
neural rod	2.81e-67	57
future spinal cord	2.81e-67	57
neural keel	2.81e-67	57
regional part of brain	1.42e-58	59
regional part of forebrain	3.54e-58	41
forebrain	3.54e-58	41
future forebrain	3.54e-58	41
central nervous system	6.85e-58	82
regional part of nervous system	2.79e-57	94
nervous system	2.79e-57	94
anterior neural tube	1.52e-56	42
brain	1.53e-54	69
future brain	1.53e-54	69
adult organism	3.31e-51	115
neural plate	4.86e-46	86
presumptive neural plate	4.86e-46	86
neurectoderm	2.31e-45	90
gray matter	8.68e-45	34
brain grey matter	8.68e-45	34
telencephalon	9.44e-45	34
regional part of telencephalon	6.21e-43	33
cerebral hemisphere	4.37e-41	32
pre-chordal neural plate	6.29e-40	61
anterior region of body	2.38e-35	129
craniocervical region	2.38e-35	129
head	9.31e-35	123
ectoderm	6.21e-30	173
presumptive ectoderm	6.21e-30	173
ectoderm-derived structure	9.00e-30	169
cerebral cortex	4.15e-28	25
pallium	4.15e-28	25
regional part of cerebral cortex	1.35e-26	22
neocortex	3.73e-26	20
basal ganglion	7.68e-19	9
nuclear complex of neuraxis	7.68e-19	9
aggregate regional part of brain	7.68e-19	9
collection of basal ganglia	7.68e-19	9
cerebral subcortex	7.68e-19	9
nucleus of brain	7.84e-19	9
neural nucleus	7.84e-19	9
telencephalic nucleus	4.67e-15	7
diencephalon	5.87e-15	7
future diencephalon	5.87e-15	7
tube	7.68e-15	194
temporal lobe	3.58e-13	7
gyrus	9.01e-13	6
anatomical conduit	1.41e-12	241
anatomical cluster	2.20e-12	286
brainstem	3.32e-12	8
posterior neural tube	4.28e-12	15
chordal neural plate	4.28e-12	15
organism subdivision	1.93e-11	365
multi-tissue structure	2.11e-11	347
organ part	3.47e-10	219
segmental subdivision of hindbrain	4.17e-10	12
hindbrain	4.17e-10	12
presumptive hindbrain	4.17e-10	12
corpus striatum	1.19e-09	4
striatum	1.19e-09	4
ventral part of telencephalon	1.19e-09	4
future corpus striatum	1.19e-09	4
segmental subdivision of nervous system	3.34e-09	13
gland of diencephalon	4.63e-09	4
neuroendocrine gland	4.63e-09	4
epithelium	4.50e-08	309
cell layer	7.32e-08	312
caudate-putamen	1.07e-07	3
dorsal striatum	1.07e-07	3
organ	1.43e-07	511
embryo	1.70e-07	612
limbic system	1.74e-07	5
middle temporal gyrus	1.76e-07	3
brainstem nucleus	3.37e-07	3
medulla oblongata	4.88e-07	3
myelencephalon	4.88e-07	3
future myelencephalon	4.88e-07	3
pons	5.40e-07	3
occipital lobe	6.51e-07	5
embryonic structure	7.49e-07	605
developing anatomical structure	7.49e-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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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.