Coexpression cluster:C4103

Full id: C4103_heart_left_diaphragm_tongue_medial_skeletal_brain

Phase1 CAGE Peaks

Hg19::chr22:41865109..41865152,+	p1@ACO2
Hg19::chr6:44194733..44194752,+	p6@SLC29A1
Hg19::chr7:44646162..44646176,+	p3@OGDH

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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p.value	FDR	nGenes	nPathway	Name
3.20096624129033e-06	0.00121078598126186	2	30	Citrate cycle (TCA cycle) (KEGG):00020
3.88503833680646e-06	0.00121078598126186	2	33	TCA Cycle (Wikipathways):WP78
5.73832218607515e-06	0.00121078598126186	2	40	Pyruvate metabolism and Citric Acid (TCA) cycle (Reactome):REACT_1046

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:0050164	oxoglutarate dehydrogenase (NADP+) activity	0.00856587778170257
GO:0006101	citrate metabolic process	0.0102180544862346
GO:0015858	nucleoside transport	0.0102180544862346
GO:0003994	aconitate hydratase activity	0.0102180544862346
GO:0004591	oxoglutarate dehydrogenase (succinyl-transferring) activity	0.0102180544862346
GO:0044262	cellular carbohydrate metabolic process	0.0102180544862346
GO:0005975	carbohydrate metabolic process	0.0176404857305316
GO:0044248	cellular catabolic process	0.0176404857305316
GO:0005337	nucleoside transmembrane transporter activity	0.0176404857305316
GO:0016624	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor	0.0176404857305316
GO:0015932	nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity	0.0176404857305316
GO:0006091	generation of precursor metabolites and energy	0.0176404857305316
GO:0009056	catabolic process	0.0176404857305316
GO:0005739	mitochondrion	0.0176404857305316
GO:0006100	tricarboxylic acid cycle intermediate metabolic process	0.0182572018144486
GO:0046356	acetyl-CoA catabolic process	0.0189659602939553
GO:0006099	tricarboxylic acid cycle	0.0189659602939553
GO:0051539	4 iron, 4 sulfur cluster binding	0.0189659602939553
GO:0006084	acetyl-CoA metabolic process	0.0189659602939553
GO:0009109	coenzyme catabolic process	0.0189659602939553
GO:0051187	cofactor catabolic process	0.0189659602939553
GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	0.0189659602939553
GO:0009060	aerobic respiration	0.0189659602939553
GO:0045333	cellular respiration	0.020666156364307
GO:0016903	oxidoreductase activity, acting on the aldehyde or oxo group of donors	0.0246182032524606
GO:0051536	iron-sulfur cluster binding	0.0274611072022562
GO:0016836	hydro-lyase activity	0.0274611072022562
GO:0051540	metal cluster binding	0.0274611072022562
GO:0016835	carbon-oxygen lyase activity	0.0296050977840218
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0296050977840218
GO:0015980	energy derivation by oxidation of organic compounds	0.0322190111754213
GO:0006096	glycolysis	0.0344012461821712
GO:0006007	glucose catabolic process	0.0369496971186839
GO:0019320	hexose catabolic process	0.0369496971186839
GO:0046365	monosaccharide catabolic process	0.0369496971186839
GO:0046164	alcohol catabolic process	0.0369496971186839
GO:0031980	mitochondrial lumen	0.0398882641926015
GO:0005759	mitochondrial matrix	0.0398882641926015
GO:0044275	cellular carbohydrate catabolic process	0.0398882641926015
GO:0016052	carbohydrate catabolic process	0.0398882641926015
GO:0006006	glucose metabolic process	0.0398882641926015

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>

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Uber Anatomy

Ontology term	p-value	n
adult organism	4.14e-36	115
neural tube	3.02e-27	57
neural rod	3.02e-27	57
future spinal cord	3.02e-27	57
neural keel	3.02e-27	57
regional part of brain	5.62e-25	59
neural plate	7.90e-25	86
presumptive neural plate	7.90e-25	86
neurectoderm	6.95e-24	90
central nervous system	2.75e-22	82
brain	6.50e-21	69
future brain	6.50e-21	69
anterior neural tube	2.78e-20	42
regional part of forebrain	6.93e-20	41
forebrain	6.93e-20	41
future forebrain	6.93e-20	41
pre-chordal neural plate	2.81e-19	61
regional part of nervous system	6.82e-19	94
nervous system	6.82e-19	94
telencephalon	4.71e-17	34
gray matter	6.39e-17	34
brain grey matter	6.39e-17	34
regional part of telencephalon	1.77e-16	33
cerebral hemisphere	3.36e-16	32
head	1.47e-14	123
anterior region of body	3.26e-14	129
craniocervical region	3.26e-14	129
multi-tissue structure	6.20e-14	347
ectoderm-derived structure	1.12e-13	169
ectoderm	1.90e-13	173
presumptive ectoderm	1.90e-13	173
tube	3.10e-13	194
regional part of cerebral cortex	3.58e-13	22
cell layer	3.92e-13	312
epithelium	6.60e-13	309
cerebral cortex	3.19e-12	25
pallium	3.19e-12	25
organ part	3.96e-12	219
neocortex	4.19e-12	20
anatomical cluster	1.26e-11	286
organism subdivision	3.25e-11	365
anatomical conduit	1.46e-10	241
multi-cellular organism	8.26e-09	659
embryo	2.03e-08	612
posterior neural tube	4.11e-08	15
chordal neural plate	4.11e-08	15
embryonic structure	1.47e-07	605
developing anatomical structure	1.47e-07	605
germ layer	2.16e-07	604
embryonic tissue	2.16e-07	604
presumptive structure	2.16e-07	604
epiblast (generic)	2.16e-07	604
segmental subdivision of nervous system	2.80e-07	13
organ	4.51e-07	511
segmental subdivision of hindbrain	5.91e-07	12
hindbrain	5.91e-07	12
presumptive hindbrain	5.91e-07	12
anatomical system	8.40e-07	625

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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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.