Coexpression cluster:C3012

Full id: C3012_cerebellum_medulla_amygdala_hippocampus_occipital_middle_parietal

Phase1 CAGE Peaks

Hg19::chr10:3146868..3146929,+	p3@PFKP
Hg19::chr17:42852832..42852834,+	p@chr17:42852832..42852834 +
Hg19::chr2:39892216..39892229,+	p17@TMEM178

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:0005945	6-phosphofructokinase complex	0.0324059715622019
GO:0003872	6-phosphofructokinase activity	0.0324059715622019
GO:0008443	phosphofructokinase activity	0.0324059715622019
GO:0019200	carbohydrate kinase activity	0.0391192555970231
GO:0005923	tight junction	0.0391192555970231
GO:0043296	apical junction complex	0.0391192555970231
GO:0016327	apicolateral plasma membrane	0.0391192555970231
GO:0006096	glycolysis	0.0391192555970231
GO:0006007	glucose catabolic process	0.0391192555970231
GO:0019320	hexose catabolic process	0.0391192555970231
GO:0046365	monosaccharide catabolic process	0.0391192555970231
GO:0046164	alcohol catabolic process	0.0391192555970231
GO:0005911	intercellular junction	0.0391192555970231
GO:0044275	cellular carbohydrate catabolic process	0.0391192555970231
GO:0044445	cytosolic part	0.0391192555970231
GO:0016052	carbohydrate catabolic process	0.0391192555970231
GO:0006006	glucose metabolic process	0.0391192555970231
GO:0019318	hexose metabolic process	0.0498895153906516
GO:0005996	monosaccharide metabolic process	0.0498895153906516

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>

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Cell Type

Ontology term	p-value	n
collagen secreting cell	6.42e-08	6
chondroblast	6.42e-08	6
chondrocyte	6.42e-08	6
skeletal muscle myoblast	5.43e-07	4
GAG secreting cell	6.43e-07	9
carbohydrate secreting cell	6.43e-07	9

Uber Anatomy

Ontology term	p-value	n
neural tube	1.39e-53	57
neural rod	1.39e-53	57
future spinal cord	1.39e-53	57
neural keel	1.39e-53	57
adult organism	1.41e-52	115
regional part of brain	3.26e-46	59
anterior neural tube	3.55e-42	42
regional part of forebrain	5.73e-41	41
forebrain	5.73e-41	41
future forebrain	5.73e-41	41
brain	1.24e-40	69
future brain	1.24e-40	69
central nervous system	2.03e-38	82
gray matter	5.47e-37	34
brain grey matter	5.47e-37	34
telencephalon	9.69e-37	34
neural plate	5.99e-36	86
presumptive neural plate	5.99e-36	86
regional part of telencephalon	2.70e-35	33
cerebral hemisphere	5.29e-34	32
neurectoderm	1.35e-33	90
regional part of nervous system	2.05e-32	94
nervous system	2.05e-32	94
regional part of cerebral cortex	9.87e-29	22
pre-chordal neural plate	2.10e-28	61
neocortex	1.07e-25	20
cerebral cortex	1.51e-24	25
pallium	1.51e-24	25
head	3.23e-24	123
anterior region of body	2.18e-23	129
craniocervical region	2.18e-23	129
tube	3.17e-18	194
ectoderm-derived structure	6.23e-16	169
anatomical conduit	3.17e-15	241
ectoderm	3.53e-15	173
presumptive ectoderm	3.53e-15	173
basal ganglion	3.33e-14	9
nuclear complex of neuraxis	3.33e-14	9
aggregate regional part of brain	3.33e-14	9
collection of basal ganglia	3.33e-14	9
cerebral subcortex	3.33e-14	9
nucleus of brain	3.77e-14	9
neural nucleus	3.77e-14	9
anatomical cluster	1.57e-13	286
brainstem	4.66e-13	8
posterior neural tube	3.07e-12	15
chordal neural plate	3.07e-12	15
telencephalic nucleus	3.09e-11	7
gyrus	7.51e-11	6
segmental subdivision of hindbrain	1.08e-10	12
hindbrain	1.08e-10	12
presumptive hindbrain	1.08e-10	12
epithelium	3.12e-10	309
temporal lobe	4.19e-10	7
cell layer	6.07e-10	312
segmental subdivision of nervous system	1.10e-09	13
limbic system	4.94e-09	5
organism subdivision	7.25e-09	365
occipital lobe	2.56e-08	5
multi-tissue structure	2.73e-08	347
organ part	3.15e-07	219
corpus striatum	4.80e-07	4
striatum	4.80e-07	4
ventral part of telencephalon	4.80e-07	4
future corpus striatum	4.80e-07	4

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)
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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.