Coexpression cluster:C1309

Full id: C1309_putamen_parietal_caudate_temporal_duodenum_Neurons_occipital

Phase1 CAGE Peaks

Hg19::chr10:26505387..26505457,+	p2@GAD2
Hg19::chr3:126113504..126113523,+	p2@CCDC37
Hg19::chrX:82763261..82763262,+	p4@POU3F4
Hg19::chrX:82763265..82763283,+	p2@POU3F4
Hg19::chrX:82763292..82763317,+	p1@POU3F4
Hg19::chrX:82763328..82763340,+	p3@POU3F4

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:0006540	glutamate decarboxylation to succinate	0.003963990479922
GO:0004351	glutamate decarboxylase activity	0.003963990479922
GO:0006105	succinate metabolic process	0.003963990479922
GO:0006538	glutamate catabolic process	0.00445942365223706
GO:0043648	dicarboxylic acid metabolic process	0.0135880239617817
GO:0042136	neurotransmitter biosynthetic process	0.0135880239617817
GO:0006536	glutamate metabolic process	0.0135880239617817
GO:0009065	glutamine family amino acid catabolic process	0.0148610260391963
GO:0050877	neurological system process	0.0156469715618911
GO:0042133	neurotransmitter metabolic process	0.0172625772989556
GO:0006100	tricarboxylic acid cycle intermediate metabolic process	0.0172625772989556
GO:0003008	system process	0.0172625772989556
GO:0048839	inner ear development	0.0173713641720009
GO:0043583	ear development	0.017827455131619
GO:0016831	carboxy-lyase activity	0.0221807032804728
GO:0001505	regulation of neurotransmitter levels	0.0258326785076236
GO:0016830	carbon-carbon lyase activity	0.0258326785076236
GO:0009064	glutamine family amino acid metabolic process	0.0258326785076236
GO:0007423	sensory organ development	0.0258326785076236
GO:0009063	amino acid catabolic process	0.0258326785076236
GO:0009310	amine catabolic process	0.0259102216636778
GO:0044270	nitrogen compound catabolic process	0.0259102216636778
GO:0030170	pyridoxal phosphate binding	0.0301957734492803
GO:0050954	sensory perception of mechanical stimulus	0.0313347330006506
GO:0007605	sensory perception of sound	0.0313347330006506
GO:0032501	multicellular organismal process	0.049157105150703

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
oligodendrocyte	5.06e-08	7
macroglial cell	5.06e-08	7
astrocyte	5.06e-08	7
oligodendrocyte precursor cell	5.06e-08	7

Uber Anatomy

Ontology term	p-value	n
neural tube	2.10e-75	57
neural rod	2.10e-75	57
future spinal cord	2.10e-75	57
neural keel	2.10e-75	57
central nervous system	2.90e-69	82
regional part of brain	8.45e-64	59
regional part of nervous system	1.83e-60	94
nervous system	1.83e-60	94
brain	2.21e-58	69
future brain	2.21e-58	69
regional part of forebrain	8.48e-57	41
forebrain	8.48e-57	41
future forebrain	8.48e-57	41
neural plate	9.48e-57	86
presumptive neural plate	9.48e-57	86
anterior neural tube	4.08e-55	42
neurectoderm	2.75e-53	90
telencephalon	7.05e-51	34
gray matter	8.90e-51	34
brain grey matter	8.90e-51	34
regional part of telencephalon	2.06e-49	33
cerebral hemisphere	2.16e-48	32
adult organism	3.78e-45	115
pre-chordal neural plate	6.12e-43	61
head	3.81e-38	123
cerebral cortex	1.59e-37	25
pallium	1.59e-37	25
ectoderm-derived structure	1.23e-35	169
anterior region of body	2.18e-35	129
craniocervical region	2.18e-35	129
ectoderm	2.94e-34	173
presumptive ectoderm	2.94e-34	173
regional part of cerebral cortex	2.23e-33	22
neocortex	1.07e-30	20
posterior neural tube	2.07e-20	15
chordal neural plate	2.07e-20	15
tube	1.17e-18	194
segmental subdivision of hindbrain	9.74e-17	12
hindbrain	9.74e-17	12
presumptive hindbrain	9.74e-17	12
segmental subdivision of nervous system	3.54e-15	13
basal ganglion	1.13e-14	9
nuclear complex of neuraxis	1.13e-14	9
aggregate regional part of brain	1.13e-14	9
collection of basal ganglia	1.13e-14	9
cerebral subcortex	1.13e-14	9
nucleus of brain	1.91e-14	9
neural nucleus	1.91e-14	9
anatomical conduit	4.59e-14	241
anatomical cluster	5.29e-14	286
organ part	3.90e-13	219
regional part of metencephalon	4.51e-13	9
metencephalon	4.51e-13	9
future metencephalon	4.51e-13	9
temporal lobe	1.98e-12	7
telencephalic nucleus	5.92e-12	7
organ	3.25e-10	511
cell layer	8.17e-10	312
organism subdivision	9.44e-10	365
gyrus	1.06e-09	6
epithelium	1.13e-09	309
cerebellum	2.04e-09	6
rhombic lip	2.04e-09	6
embryo	2.16e-09	612
multi-tissue structure	2.94e-09	347
brainstem	1.05e-08	8
parietal lobe	1.19e-08	5
occipital lobe	1.19e-08	5
limbic system	1.50e-08	5
corpus striatum	5.83e-08	4
striatum	5.83e-08	4
ventral part of telencephalon	5.83e-08	4
future corpus striatum	5.83e-08	4
germ layer	1.07e-07	604
embryonic tissue	1.07e-07	604
presumptive structure	1.07e-07	604
epiblast (generic)	1.07e-07	604
embryonic structure	1.24e-07	605
developing anatomical structure	1.24e-07	605
diencephalon	1.63e-07	7
future diencephalon	1.63e-07	7
dorsal region element	3.57e-07	5
dorsum	3.57e-07	5
multi-cellular organism	8.51e-07	659
anatomical system	8.68e-07	625
anatomical group	9.94e-07	626

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
SP1#6667	4	3.7989209187606	0.0105224661679851	0.0389396869151085

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.