Coexpression cluster:C1858

Full id: C1858_Hepatocyte_parotid_salivary_submaxillary_liver_small_cerebellum

Phase1 CAGE Peaks

Hg19::chr1:41454160..41454176,+	p6@CTPS
Hg19::chr1:41454185..41454224,+	p5@CTPS
Hg19::chr1:41454251..41454260,+	p21@CTPS
Hg19::chr6:46620445..46620463,-	p1@CYP39A1
Hg19::chr6:46620465..46620476,-	p3@CYP39A1

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:0033782	24-hydroxycholesterol 7alpha-hydroxylase activity	0.00300247262451431
GO:0008387	steroid 7-alpha-hydroxylase activity	0.00300247262451431
GO:0008396	oxysterol 7-alpha-hydroxylase activity	0.00360286108933212
GO:0003883	CTP synthase activity	0.00360286108933212
GO:0030573	bile acid catabolic process	0.00360286108933212
GO:0006699	bile acid biosynthetic process	0.00500345816532559
GO:0006707	cholesterol catabolic process	0.00500345816532559
GO:0016127	sterol catabolic process	0.00500345816532559
GO:0019752	carboxylic acid metabolic process	0.00500345816532559
GO:0006082	organic acid metabolic process	0.00500345816532559
GO:0046395	carboxylic acid catabolic process	0.00500345816532559
GO:0016054	organic acid catabolic process	0.00500345816532559
GO:0008206	bile acid metabolic process	0.00643254415861032
GO:0008395	steroid hydroxylase activity	0.00643254415861032
GO:0006706	steroid catabolic process	0.00680400192983605
GO:0006541	glutamine metabolic process	0.00937941257394925
GO:0016709	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen	0.0102888888512249
GO:0046036	CTP metabolic process	0.0102888888512249
GO:0009209	pyrimidine ribonucleoside triphosphate biosynthetic process	0.0102888888512249
GO:0009208	pyrimidine ribonucleoside triphosphate metabolic process	0.0102888888512249
GO:0006241	CTP biosynthetic process	0.0102888888512249
GO:0009220	pyrimidine ribonucleotide biosynthetic process	0.0106981654968376
GO:0009218	pyrimidine ribonucleotide metabolic process	0.0106981654968376
GO:0044242	cellular lipid catabolic process	0.0120012289244444
GO:0009147	pyrimidine nucleoside triphosphate metabolic process	0.0120012289244444
GO:0006221	pyrimidine nucleotide biosynthetic process	0.0122314812898656
GO:0044249	cellular biosynthetic process	0.0122882589398147
GO:0042493	response to drug	0.0134987973254267
GO:0006220	pyrimidine nucleotide metabolic process	0.0142733285258762
GO:0008203	cholesterol metabolic process	0.0150851187339486
GO:0009064	glutamine family amino acid metabolic process	0.0150851187339486
GO:0016053	organic acid biosynthetic process	0.0150851187339486
GO:0046394	carboxylic acid biosynthetic process	0.0150851187339486
GO:0009058	biosynthetic process	0.0152499402383358
GO:0006694	steroid biosynthetic process	0.0152499402383358
GO:0016125	sterol metabolic process	0.015396771212381
GO:0007586	digestion	0.015396771212381
GO:0009201	ribonucleoside triphosphate biosynthetic process	0.0190872381079814
GO:0009142	nucleoside triphosphate biosynthetic process	0.0193648990451604
GO:0009199	ribonucleoside triphosphate metabolic process	0.0197781111761532
GO:0016042	lipid catabolic process	0.0209721444520474
GO:0009141	nucleoside triphosphate metabolic process	0.0209721444520474
GO:0009260	ribonucleotide biosynthetic process	0.0218746911107329
GO:0005792	microsome	0.0220070949015963
GO:0042598	vesicular fraction	0.0220070949015963
GO:0009259	ribonucleotide metabolic process	0.0220070949015963
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.0225557870057453
GO:0008202	steroid metabolic process	0.0278068183692588
GO:0004497	monooxygenase activity	0.028456624280113
GO:0009165	nucleotide biosynthetic process	0.0305107289082287
GO:0032787	monocarboxylic acid metabolic process	0.0328298187167133
GO:0020037	heme binding	0.0328298187167133
GO:0046906	tetrapyrrole binding	0.0328298187167133
GO:0008610	lipid biosynthetic process	0.0368495454127848
GO:0009117	nucleotide metabolic process	0.0369362602454575
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0388719701314618
GO:0016879	ligase activity, forming carbon-nitrogen bonds	0.0388719701314618
GO:0006066	alcohol metabolic process	0.0457713421174718
GO:0005789	endoplasmic reticulum membrane	0.0463011143602194
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0463365297057089
GO:0006520	amino acid metabolic process	0.0463365297057089
GO:0005506	iron ion binding	0.0483575825870521
GO:0044432	endoplasmic reticulum part	0.0491860097835861

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
endodermal cell	7.22e-09	59
epithelial cell	3.92e-07	254

Uber Anatomy

Ontology term	p-value	n
digestive system	8.98e-27	155
digestive tract	8.98e-27	155
primitive gut	8.98e-27	155
endoderm-derived structure	1.70e-25	169
endoderm	1.70e-25	169
presumptive endoderm	1.70e-25	169
subdivision of digestive tract	4.93e-24	129
endodermal part of digestive tract	4.93e-24	129
adult organism	1.12e-20	115
mixed endoderm/mesoderm-derived structure	1.13e-17	130
multi-tissue structure	2.54e-17	347
organ	2.44e-15	511
gland	2.40e-14	59
foregut	9.70e-14	98
primordium	3.29e-11	168
respiratory system	9.66e-11	72
endo-epithelium	1.10e-10	82
anatomical cluster	4.37e-10	286
orifice	1.42e-09	35
exocrine gland	1.49e-09	31
exocrine system	1.49e-09	31
immaterial anatomical entity	3.36e-09	126
gut epithelium	3.57e-09	54
organism subdivision	6.53e-09	365
mesenchyme	8.68e-09	238
entire embryonic mesenchyme	8.68e-09	238
anatomical system	1.36e-08	625
organ segment	1.44e-08	97
anatomical group	1.78e-08	626
multi-cellular organism	2.70e-08	659
organ part	8.81e-08	219
anterior region of body	9.89e-08	129
craniocervical region	9.89e-08	129
embryo	1.14e-07	612
gastrointestinal system	2.28e-07	35
endocrine gland	4.52e-07	35
head	4.59e-07	123
germ layer	5.97e-07	604
embryonic tissue	5.97e-07	604
presumptive structure	5.97e-07	604
epiblast (generic)	5.97e-07	604
respiratory tract	7.41e-07	53
embryonic structure	7.57e-07	605
developing anatomical structure	7.57e-07	605

Disease

Ontology term	p-value	n
carcinoma	3.69e-13	106
cell type cancer	1.44e-08	143

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.