Coexpression cluster:C3729

Full id: C3729_medial_hippocampus_cerebral_middle_parietal_globus_olfactory

Phase1 CAGE Peaks

Hg19::chr18:55030190..55030203,+	p@chr18:55030190..55030203 +
Hg19::chr3:48016734..48016748,-	p49@MAP4
Hg19::chr7:98460933..98460941,-	p19@TMEM130

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:0007026	negative regulation of microtubule depolymerization	0.0169474033792886
GO:0031114	regulation of microtubule depolymerization	0.0169474033792886
GO:0007019	microtubule depolymerization	0.0169474033792886
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.0169474033792886
GO:0031110	regulation of microtubule polymerization or depolymerization	0.0169474033792886
GO:0031109	microtubule polymerization or depolymerization	0.0169474033792886
GO:0051261	protein depolymerization	0.0206485650106885
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0206485650106885
GO:0051128	regulation of cellular component organization and biogenesis	0.0300112721168847
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0300112721168847
GO:0051248	negative regulation of protein metabolic process	0.0300112721168847
GO:0005875	microtubule associated complex	0.0475606955091801

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	3.99e-64	57
neural rod	3.99e-64	57
future spinal cord	3.99e-64	57
neural keel	3.99e-64	57
central nervous system	5.51e-54	82
regional part of nervous system	3.77e-53	94
nervous system	3.77e-53	94
regional part of brain	1.95e-52	59
regional part of forebrain	1.41e-49	41
forebrain	1.41e-49	41
future forebrain	1.41e-49	41
anterior neural tube	3.50e-48	42
brain	3.00e-47	69
future brain	3.00e-47	69
gray matter	1.26e-46	34
brain grey matter	1.26e-46	34
telencephalon	4.48e-46	34
neural plate	1.95e-44	86
presumptive neural plate	1.95e-44	86
regional part of telencephalon	4.28e-44	33
cerebral hemisphere	8.25e-43	32
neurectoderm	7.25e-42	90
adult organism	1.38e-38	115
regional part of cerebral cortex	1.88e-33	22
pre-chordal neural plate	3.18e-32	61
neocortex	4.12e-29	20
cerebral cortex	6.66e-29	25
pallium	6.66e-29	25
ectoderm-derived structure	1.03e-26	169
head	1.15e-26	123
anterior region of body	4.60e-26	129
craniocervical region	4.60e-26	129
ectoderm	9.50e-26	173
presumptive ectoderm	9.50e-26	173
nucleus of brain	5.15e-20	9
neural nucleus	5.15e-20	9
posterior neural tube	2.30e-16	15
chordal neural plate	2.30e-16	15
telencephalic nucleus	8.67e-16	7
basal ganglion	8.80e-16	9
nuclear complex of neuraxis	8.80e-16	9
aggregate regional part of brain	8.80e-16	9
collection of basal ganglia	8.80e-16	9
cerebral subcortex	8.80e-16	9
temporal lobe	1.42e-14	7
tube	5.17e-14	194
brainstem	6.12e-13	8
segmental subdivision of nervous system	6.31e-13	13
organ part	3.86e-12	219
anatomical conduit	1.91e-11	241
segmental subdivision of hindbrain	3.86e-11	12
hindbrain	3.86e-11	12
presumptive hindbrain	3.86e-11	12
gyrus	2.58e-10	6
corpus striatum	3.89e-10	4
striatum	3.89e-10	4
ventral part of telencephalon	3.89e-10	4
future corpus striatum	3.89e-10	4
anatomical cluster	6.94e-10	286
epithelium	1.19e-08	309
middle temporal gyrus	1.54e-08	3
cell layer	1.93e-08	312
caudate-putamen	3.27e-08	3
dorsal striatum	3.27e-08	3
limbic system	3.28e-08	5
parietal lobe	6.71e-08	5
occipital lobe	7.20e-08	5
pons	8.77e-08	3
organism subdivision	1.54e-07	365
brainstem nucleus	1.71e-07	3
spinal cord	1.79e-07	3
organ	1.93e-07	511
germ layer	2.69e-07	604
embryonic tissue	2.69e-07	604
presumptive structure	2.69e-07	604
epiblast (generic)	2.69e-07	604
medulla oblongata	2.96e-07	3
myelencephalon	2.96e-07	3
future myelencephalon	2.96e-07	3
embryonic structure	2.98e-07	605
developing anatomical structure	2.98e-07	605
embryo	6.15e-07	612
anatomical system	7.49e-07	625
anatomical group	8.28e-07	626

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.