Coexpression cluster:C3632

Full id: C3632_optic_spinal_occipital_diencephalon_brain_cerebral_thalamus

Phase1 CAGE Peaks

Hg19::chr17:40126534..40126547,+	p4@BC148241
Hg19::chr17:42985456..42985481,-	p24@GFAP
Hg19::chr19:36360601..36360612,+	p7@APLP1

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:0006378	mRNA polyadenylation	0.0280177159022779
GO:0043631	RNA polyadenylation	0.0280177159022779
GO:0031124	mRNA 3'-end processing	0.0280177159022779
GO:0031123	RNA 3'-end processing	0.0285159331518258
GO:0005905	coated pit	0.0394349325440851
GO:0030198	extracellular matrix organization and biogenesis	0.0394349325440851
GO:0030900	forebrain development	0.0394349325440851
GO:0005604	basement membrane	0.0463444807873957
GO:0008201	heparin binding	0.0463444807873957
GO:0043062	extracellular structure organization and biogenesis	0.0463444807873957
GO:0005200	structural constituent of cytoskeleton	0.0463444807873957
GO:0005539	glycosaminoglycan binding	0.0489995305385511
GO:0030247	polysaccharide binding	0.0489995305385511
GO:0005507	copper ion binding	0.0489995305385511
GO:0001871	pattern binding	0.0489995305385511
GO:0044420	extracellular matrix part	0.0489995305385511
GO:0007420	brain development	0.0489995305385511

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	6.38e-36	57
neural rod	6.38e-36	57
future spinal cord	6.38e-36	57
neural keel	6.38e-36	57
central nervous system	1.36e-34	82
regional part of nervous system	9.53e-33	94
nervous system	9.53e-33	94
regional part of brain	8.55e-30	59
brain	4.12e-29	69
future brain	4.12e-29	69
neural plate	2.66e-27	86
presumptive neural plate	2.66e-27	86
neurectoderm	5.30e-27	90
regional part of forebrain	3.42e-26	41
forebrain	3.42e-26	41
future forebrain	3.42e-26	41
anterior neural tube	3.41e-25	42
gray matter	3.92e-24	34
brain grey matter	3.92e-24	34
telencephalon	4.82e-24	34
regional part of telencephalon	3.15e-23	33
cerebral hemisphere	4.07e-22	32
pre-chordal neural plate	3.37e-20	61
cerebral cortex	3.23e-16	25
pallium	3.23e-16	25
head	7.78e-16	123
ectoderm	1.99e-15	173
presumptive ectoderm	1.99e-15	173
ectoderm-derived structure	2.86e-15	169
adult organism	1.12e-14	115
anterior region of body	1.52e-14	129
craniocervical region	1.52e-14	129
regional part of cerebral cortex	1.23e-13	22
neocortex	6.37e-12	20
posterior neural tube	8.94e-12	15
chordal neural plate	8.94e-12	15
segmental subdivision of nervous system	7.18e-10	13
nucleus of brain	1.32e-09	9
neural nucleus	1.32e-09	9
basal ganglion	1.50e-09	9
nuclear complex of neuraxis	1.50e-09	9
aggregate regional part of brain	1.50e-09	9
collection of basal ganglia	1.50e-09	9
cerebral subcortex	1.50e-09	9
segmental subdivision of hindbrain	6.72e-09	12
hindbrain	6.72e-09	12
presumptive hindbrain	6.72e-09	12
telencephalic nucleus	9.81e-08	7
organ part	5.44e-07	219
tube	8.75e-07	194
brainstem	9.46e-07	8

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.