Coexpression cluster:C841

Full id: C841_cerebellum_occipital_medial_parietal_middle_caudate_globus

Phase1 CAGE Peaks

Hg19::chr16:80838247..80838258,-	p8@CDYL2
Hg19::chr19:49149232..49149245,+	p@chr19:49149232..49149245 +
Hg19::chr19:6494729..6494749,+	p@chr19:6494729..6494749 +
Hg19::chr20:10288445..10288449,+	p@chr20:10288445..10288449 +
Hg19::chr3:120776122..120776137,+	p@chr3:120776122..120776137 +
Hg19::chr3:183543817..183543832,-	p5@MAP6D1
Hg19::chrX:139866190..139866197,-	p5@CDR1
Hg19::chrX:139866214..139866221,+	p@chrX:139866214..139866221 +
Hg19::chrX:139866339..139866349,+	p@chrX:139866339..139866349 +
Hg19::chrX:153094936..153094950,-	p@chrX:153094936..153094950 -

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0018318	protein amino acid palmitoylation	0.00123631225715295
GO:0018009	N-terminal peptidyl-L-cysteine N-palmitoylation	0.00123631225715295
GO:0006500	N-terminal protein palmitoylation	0.00123631225715295
GO:0018198	peptidyl-cysteine modification	0.00123631225715295
GO:0018345	protein palmitoylation	0.00395602453569053
GO:0006498	N-terminal protein lipidation	0.00576894769571694
GO:0005801	cis-Golgi network	0.00847619722105734
GO:0018409	peptide or protein amino-terminal blocking	0.0086525299109976
GO:0031365	N-terminal protein amino acid modification	0.00874645367489492
GO:0007026	negative regulation of microtubule depolymerization	0.00874645367489492
GO:0031114	regulation of microtubule depolymerization	0.00874645367489492
GO:0007019	microtubule depolymerization	0.00874645367489492
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.00874645367489492
GO:0031110	regulation of microtubule polymerization or depolymerization	0.00988598530458499
GO:0043543	protein amino acid acylation	0.00988598530458499
GO:0031109	microtubule polymerization or depolymerization	0.00988598530458499
GO:0006996	organelle organization and biogenesis	0.00996380673908192
GO:0051261	protein depolymerization	0.0123532964165906
GO:0008017	microtubule binding	0.0123532964165906
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0123532964165906
GO:0006497	protein amino acid lipidation	0.0123532964165906
GO:0042158	lipoprotein biosynthetic process	0.0123532964165906
GO:0015631	tubulin binding	0.0142033612291807
GO:0005798	Golgi-associated vesicle	0.0142033612291807
GO:0042157	lipoprotein metabolic process	0.0165957380836218
GO:0051128	regulation of cellular component organization and biogenesis	0.0183402218492073
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0183402218492073
GO:0051248	negative regulation of protein metabolic process	0.0183402218492073
GO:0003682	chromatin binding	0.0199106091636198
GO:0018193	peptidyl-amino acid modification	0.0199106091636198
GO:0005516	calmodulin binding	0.0224465584136513
GO:0016043	cellular component organization and biogenesis	0.0244185682156788
GO:0044446	intracellular organelle part	0.0365061351107608
GO:0044422	organelle part	0.0365061351107608
GO:0006333	chromatin assembly or disassembly	0.0384185189393315
GO:0007017	microtubule-based process	0.0428336985479389
GO:0000785	chromatin	0.0428336985479389
GO:0016023	cytoplasmic membrane-bound vesicle	0.0444034554120826
GO:0031988	membrane-bound vesicle	0.0444034554120826
GO:0044431	Golgi apparatus part	0.0484884833151138
GO:0051246	regulation of protein metabolic process	0.0484884833151138
GO:0031410	cytoplasmic vesicle	0.0484884833151138
GO:0031982	vesicle	0.0484884833151138
GO:0009892	negative regulation of metabolic process	0.0484884833151138
GO:0006325	establishment and/or maintenance of chromatin architecture	0.0484884833151138
GO:0006323	DNA packaging	0.0484884833151138
GO:0044427	chromosomal part	0.0484884833151138

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>

---

Uber Anatomy

Ontology term	p-value	n
neural tube	3.43e-35	57
neural rod	3.43e-35	57
future spinal cord	3.43e-35	57
neural keel	3.43e-35	57
regional part of nervous system	3.64e-33	94
nervous system	3.64e-33	94
regional part of brain	1.96e-32	59
central nervous system	1.08e-31	82
neurectoderm	1.62e-30	90
neural plate	3.30e-30	86
presumptive neural plate	3.30e-30	86
brain	4.49e-29	69
future brain	4.49e-29	69
anterior neural tube	3.17e-26	42
regional part of forebrain	7.29e-26	41
forebrain	7.29e-26	41
future forebrain	7.29e-26	41
adult organism	4.02e-24	115
gray matter	1.95e-22	34
brain grey matter	1.95e-22	34
telencephalon	2.41e-22	34
regional part of telencephalon	1.14e-21	33
pre-chordal neural plate	4.07e-21	61
cerebral hemisphere	6.05e-21	32
ectoderm	5.40e-18	173
presumptive ectoderm	5.40e-18	173
regional part of cerebral cortex	1.01e-17	22
ectoderm-derived structure	1.88e-17	169
head	6.32e-17	123
anterior region of body	7.10e-17	129
craniocervical region	7.10e-17	129
neocortex	2.38e-16	20
cerebral cortex	5.52e-16	25
pallium	5.52e-16	25
posterior neural tube	5.74e-10	15
chordal neural plate	5.74e-10	15
organism subdivision	1.85e-09	365
tube	3.71e-09	194
segmental subdivision of nervous system	1.07e-08	13
segmental subdivision of hindbrain	5.00e-08	12
hindbrain	5.00e-08	12
presumptive hindbrain	5.00e-08	12
nucleus of brain	5.72e-08	9
neural nucleus	5.72e-08	9
basal ganglion	5.94e-08	9
nuclear complex of neuraxis	5.94e-08	9
aggregate regional part of brain	5.94e-08	9
collection of basal ganglia	5.94e-08	9
cerebral subcortex	5.94e-08	9
temporal lobe	3.99e-07	7
organ part	5.76e-07	219
brainstem	9.23e-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

---

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

---

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

---

This analysis result is provided for C0 - C305 clusters.