Coexpression cluster:C4634

Full id: C4634_melanoma_occipital_amygdala_temporal_postcentral_brain_insula

Phase1 CAGE Peaks

Hg19::chr7:100808320..100808338,-	p3@VGF
Hg19::chr7:100808394..100808436,-	p2@VGF
Hg19::chr9:137967395..137967412,+	p2@OLFM1

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:0001541	ovarian follicle development	0.0114354058803748
GO:0016524	latrotoxin receptor activity	0.0114354058803748
GO:0022601	menstrual cycle phase	0.0114354058803748
GO:0022602	menstrual cycle process	0.0114354058803748
GO:0008585	female gonad development	0.0114354058803748
GO:0046660	female sex differentiation	0.0114354058803748
GO:0046545	development of primary female sexual characteristics	0.0114354058803748
GO:0042698	menstrual cycle	0.0114354058803748
GO:0005184	neuropeptide hormone activity	0.0114354058803748
GO:0048731	system development	0.0117358057120867
GO:0008406	gonad development	0.0117358057120867
GO:0048608	reproductive structure development	0.0117358057120867
GO:0048856	anatomical structure development	0.0117358057120867
GO:0045137	development of primary sexual characteristics	0.0117358057120867
GO:0032504	multicellular organism reproduction	0.0117358057120867
GO:0048609	reproductive process in a multicellular organism	0.0117358057120867
GO:0005788	endoplasmic reticulum lumen	0.0117358057120867
GO:0007275	multicellular organismal development	0.0132863134972843
GO:0007548	sex differentiation	0.0132863134972843
GO:0003006	reproductive developmental process	0.013555761989149
GO:0032502	developmental process	0.0244911273801044
GO:0032501	multicellular organismal process	0.0293449752098031
GO:0005179	hormone activity	0.0293449752098031
GO:0008083	growth factor activity	0.0327702848493947
GO:0022414	reproductive process	0.0362342900506413
GO:0044444	cytoplasmic part	0.0362342900506413
GO:0019953	sexual reproduction	0.0362342900506413
GO:0031410	cytoplasmic vesicle	0.0461856130606856
GO:0031982	vesicle	0.0461856130606856

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
neuron	6.05e-12	6
neuroblast	6.05e-12	6
electrically signaling cell	6.05e-12	6
neuronal stem cell	1.35e-11	8
embryonic stem cell	4.20e-10	5

Uber Anatomy

Ontology term	p-value	n
central nervous system	2.33e-65	81
nervous system	2.65e-64	89
neural tube	3.17e-60	56
neural rod	3.17e-60	56
future spinal cord	3.17e-60	56
neural keel	3.17e-60	56
regional part of nervous system	2.23e-58	53
regional part of brain	2.23e-58	53
regional part of forebrain	4.25e-54	41
forebrain	4.25e-54	41
anterior neural tube	4.25e-54	41
future forebrain	4.25e-54	41
cerebral hemisphere	9.64e-52	32
telencephalon	1.48e-51	34
brain grey matter	3.63e-51	34
gray matter	3.63e-51	34
brain	1.27e-49	68
future brain	1.27e-49	68
regional part of telencephalon	7.48e-48	32
neurectoderm	4.64e-44	86
regional part of cerebral cortex	1.60e-43	22
neural plate	9.26e-41	82
presumptive neural plate	9.26e-41	82
neocortex	2.44e-39	20
cerebral cortex	1.18e-37	25
pallium	1.18e-37	25
pre-chordal neural plate	5.24e-37	61
ectoderm-derived structure	6.79e-35	171
ectoderm	6.79e-35	171
presumptive ectoderm	6.79e-35	171
ecto-epithelium	7.17e-33	104
adult organism	2.88e-26	114
structure with developmental contribution from neural crest	8.01e-23	132
organ system subdivision	1.03e-19	223
basal ganglion	1.69e-15	9
nuclear complex of neuraxis	1.69e-15	9
aggregate regional part of brain	1.69e-15	9
collection of basal ganglia	1.69e-15	9
cerebral subcortex	1.69e-15	9
neural nucleus	1.06e-14	9
nucleus of brain	1.06e-14	9
gyrus	1.08e-13	6
limbic system	5.58e-12	5
temporal lobe	1.21e-11	6
parietal lobe	1.27e-11	5
telencephalic nucleus	1.62e-11	7
occipital lobe	2.00e-11	5
brainstem	2.35e-11	6
tube	2.85e-10	192
corpus striatum	5.09e-10	4
striatum	5.09e-10	4
ventral part of telencephalon	5.09e-10	4
future corpus striatum	5.09e-10	4
posterior neural tube	9.87e-09	15
chordal neural plate	9.87e-09	15
caudate-putamen	6.57e-08	3
dorsal striatum	6.57e-08	3
frontal cortex	1.30e-07	3
anatomical cluster	1.88e-07	373
segmental subdivision of hindbrain	5.84e-07	12
hindbrain	5.84e-07	12
presumptive hindbrain	5.84e-07	12

Disease

Ontology term	p-value	n
germ cell and embryonal cancer	9.74e-10	22
germ cell cancer	9.74e-10	22
neuroectodermal tumor	2.57e-08	10

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.