Coexpression cluster:C3285

Full id: C3285_cerebellum_parietal_medial_middle_hippocampus_olfactory_occipital

Phase1 CAGE Peaks

Hg19::chr12:5023276..5023280,+	p1@AK124568
Hg19::chr3:121026029..121026045,+	p@chr3:121026029..121026045 +
Hg19::chr9:140637461..140637472,+	p5@EHMT1

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:0015079	potassium ion transmembrane transporter activity	0.018190916284373
GO:0016571	histone methylation	0.0204575515773574
GO:0005251	delayed rectifier potassium channel activity	0.0204575515773574
GO:0008213	protein amino acid alkylation	0.0204575515773574
GO:0006479	protein amino acid methylation	0.0204575515773574
GO:0018024	histone-lysine N-methyltransferase activity	0.0204575515773574
GO:0016278	lysine N-methyltransferase activity	0.0204575515773574
GO:0016279	protein-lysine N-methyltransferase activity	0.0204575515773574
GO:0042054	histone methyltransferase activity	0.0216408714849049
GO:0043414	biopolymer methylation	0.0216408714849049
GO:0016570	histone modification	0.0216408714849049
GO:0008276	protein methyltransferase activity	0.0216408714849049
GO:0008170	N-methyltransferase activity	0.0216408714849049
GO:0016569	covalent chromatin modification	0.0216408714849049
GO:0032259	methylation	0.0290759064854089
GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	0.03255224172755
GO:0008076	voltage-gated potassium channel complex	0.0437947199420364
GO:0030955	potassium ion binding	0.045368852072499
GO:0006730	one-carbon compound metabolic process	0.045368852072499
GO:0003012	muscle system process	0.045368852072499
GO:0005249	voltage-gated potassium channel activity	0.045368852072499
GO:0006936	muscle contraction	0.045368852072499

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	4.88e-86	57
neural rod	4.88e-86	57
future spinal cord	4.88e-86	57
neural keel	4.88e-86	57
regional part of brain	4.30e-75	59
brain	1.65e-74	69
future brain	1.65e-74	69
central nervous system	7.99e-70	82
regional part of forebrain	7.94e-68	41
forebrain	7.94e-68	41
future forebrain	7.94e-68	41
neural plate	2.13e-66	86
presumptive neural plate	2.13e-66	86
anterior neural tube	5.19e-66	42
adult organism	6.85e-66	115
regional part of nervous system	1.29e-63	94
nervous system	1.29e-63	94
neurectoderm	7.12e-63	90
gray matter	9.16e-60	34
brain grey matter	9.16e-60	34
telencephalon	2.27e-59	34
regional part of telencephalon	7.39e-57	33
cerebral hemisphere	3.20e-55	32
pre-chordal neural plate	1.14e-50	61
head	2.94e-44	123
regional part of cerebral cortex	5.21e-44	22
anterior region of body	1.35e-41	129
craniocervical region	1.35e-41	129
neocortex	5.38e-39	20
cerebral cortex	3.05e-38	25
pallium	3.05e-38	25
ectoderm-derived structure	9.66e-36	169
ectoderm	1.35e-34	173
presumptive ectoderm	1.35e-34	173
nucleus of brain	1.75e-23	9
neural nucleus	1.75e-23	9
basal ganglion	2.74e-23	9
nuclear complex of neuraxis	2.74e-23	9
aggregate regional part of brain	2.74e-23	9
collection of basal ganglia	2.74e-23	9
cerebral subcortex	2.74e-23	9
tube	4.46e-21	194
posterior neural tube	4.29e-20	15
chordal neural plate	4.29e-20	15
telencephalic nucleus	2.01e-18	7
segmental subdivision of hindbrain	2.22e-17	12
hindbrain	2.22e-17	12
presumptive hindbrain	2.22e-17	12
gyrus	3.13e-17	6
organ part	1.10e-16	219
temporal lobe	2.53e-16	7
segmental subdivision of nervous system	6.84e-16	13
anatomical cluster	1.25e-15	286
brainstem	1.63e-15	8
anatomical conduit	2.20e-15	241
epithelium	3.47e-14	309
limbic system	4.52e-14	5
cell layer	6.48e-14	312
corpus striatum	1.04e-11	4
striatum	1.04e-11	4
ventral part of telencephalon	1.04e-11	4
future corpus striatum	1.04e-11	4
regional part of metencephalon	3.60e-11	9
metencephalon	3.60e-11	9
future metencephalon	3.60e-11	9
diencephalon	8.90e-10	7
future diencephalon	8.90e-10	7
middle temporal gyrus	1.11e-09	3
occipital lobe	2.22e-09	5
pons	2.49e-09	3
organism subdivision	2.68e-09	365
caudate-putamen	3.02e-09	3
dorsal striatum	3.02e-09	3
parietal lobe	3.69e-09	5
organ	7.52e-09	511
brainstem nucleus	1.15e-08	3
medulla oblongata	2.32e-08	3
myelencephalon	2.32e-08	3
future myelencephalon	2.32e-08	3
frontal cortex	5.97e-07	2
multi-tissue structure	8.49e-07	347
dorsal plus ventral thalamus	9.08e-07	2
locus ceruleus	9.59e-07	2
hindbrain nucleus	9.59e-07	2
caudate nucleus	9.86e-07	2
future caudate nucleus	9.86e-07	2

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.