Coexpression cluster:C693

Full id: C693_cerebellum_medulla_spinal_locus_Hepatocyte_pons_thalamus

Phase1 CAGE Peaks

Hg19::chr11:7369947..7369952,+	p@chr11:7369947..7369952 +
Hg19::chr12:109273861..109273889,+	p1@DAO
Hg19::chr19:29493456..29493477,+	p1@LOC100505835
Hg19::chr19:29493486..29493497,+	p2@LOC100505835
Hg19::chr1:90885631..90885647,-	p@chr1:90885631..90885647 -
Hg19::chr1:90885681..90885693,-	p@chr1:90885681..90885693 -
Hg19::chr3:125997081..125997085,+	p@chr3:125997081..125997085 +
Hg19::chr3:147111505..147111529,+	p6@ZIC1
Hg19::chr6:138959791..138959803,-	p@chr6:138959791..138959803 -
Hg19::chr9:73736331..73736347,-	p3@TRPM3
Hg19::chrX:106692537..106692551,+	p@chrX:106692537..106692551 +
Hg19::chrX:106692569..106692585,+	p@chrX:106692569..106692585 +

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:0003884	D-amino-acid oxidase activity	0.0358467233571613
GO:0008589	regulation of smoothened signaling pathway	0.0358467233571613
GO:0007224	smoothened signaling pathway	0.0453250397872941
GO:0016641	oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor	0.0453250397872941
GO:0042472	inner ear morphogenesis	0.0453250397872941
GO:0016638	oxidoreductase activity, acting on the CH-NH2 group of donors	0.0453250397872941
GO:0042471	ear morphogenesis	0.0453250397872941
GO:0048839	inner ear development	0.0477464012889728
GO:0043583	ear development	0.0477464012889728

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><br>

---

Cell Type

Ontology term	p-value	n
neural cell	6.35e-10	25
neuron associated cell	1.34e-07	17
neuron associated cell (sensu Vertebrata)	1.34e-07	17
skin fibroblast	8.50e-07	23
glial cell (sensu Vertebrata)	8.70e-07	15
glial cell	8.70e-07	15
glioblast	8.70e-07	15
glioblast (sensu Vertebrata)	8.70e-07	15

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	5.76e-55	94
nervous system	5.76e-55	94
central nervous system	2.28e-53	82
brain	1.45e-46	69
future brain	1.45e-46	69
neural tube	9.59e-43	57
neural rod	9.59e-43	57
future spinal cord	9.59e-43	57
neural keel	9.59e-43	57
regional part of brain	4.73e-41	59
neural plate	2.21e-34	86
presumptive neural plate	2.21e-34	86
neurectoderm	8.34e-34	90
anterior neural tube	2.21e-30	42
regional part of forebrain	7.96e-30	41
forebrain	7.96e-30	41
future forebrain	7.96e-30	41
adult organism	3.05e-27	115
ectoderm	1.67e-26	173
presumptive ectoderm	1.67e-26	173
ectoderm-derived structure	1.83e-26	169
pre-chordal neural plate	5.52e-25	61
gray matter	1.07e-24	34
brain grey matter	1.07e-24	34
telencephalon	1.33e-24	34
regional part of telencephalon	8.31e-24	33
head	3.20e-23	123
cerebral hemisphere	7.07e-23	32
anterior region of body	3.07e-22	129
craniocervical region	3.07e-22	129
cerebral cortex	3.44e-17	25
pallium	3.44e-17	25
regional part of cerebral cortex	2.43e-16	22
organism subdivision	5.43e-15	365
neocortex	1.10e-14	20
posterior neural tube	3.08e-13	15
chordal neural plate	3.08e-13	15
segmental subdivision of nervous system	2.08e-11	13
segmental subdivision of hindbrain	1.14e-10	12
hindbrain	1.14e-10	12
presumptive hindbrain	1.14e-10	12
nucleus of brain	4.55e-09	9
neural nucleus	4.55e-09	9
basal ganglion	7.40e-09	9
nuclear complex of neuraxis	7.40e-09	9
aggregate regional part of brain	7.40e-09	9
collection of basal ganglia	7.40e-09	9
cerebral subcortex	7.40e-09	9
brainstem	3.32e-08	8
regional part of metencephalon	5.07e-08	9
metencephalon	5.07e-08	9
future metencephalon	5.07e-08	9
multi-cellular organism	1.99e-07	659
tube	2.02e-07	194
cell layer	2.47e-07	312
telencephalic nucleus	2.48e-07	7
epithelium	3.97e-07	309

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.