EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000160200 (Gene tree)
Gene ID: 875
Gene Symbol: CBS
Alias: HIP4
Full Name: cystathionine-beta-synthase
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Minus strand
Length: 23,753 bases
Position: chr21:43,053,191-43,076,943
Accession: 1550
RBP type: non-canonical RBP
Summary: The protein encoded by this gene acts as a homotetramer to catalyze the conversion of homocysteine to cystathionine, the first step in the transsulfuration pathway. The encoded protein is allosterically activated by adenosyl-methionine and uses pyridoxal phosphate as a cofactor. Defects in this gene can cause cystathionine beta-synthase deficiency (CBSD), which can lead to homocystinuria. This gene is a major contributor to cellular hydrogen sulfide production. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Feb 2016]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
29431736	Capturing the interactome of newly transcribed RNA	PolyT-RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & MCF7	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000462349	CBS-210	1038	-	-	- (aa)	-	-
ENST00000486098	CBS-214	773	-	-	- (aa)	-	-
ENST00000451248	CBS-207	573	-	ENSP00000402823	149 (aa)	-	H7C1W6
ENST00000478709	CBS-213	727	-	-	- (aa)	-	-
ENST00000461686	CBS-209	2656	-	-	- (aa)	-	-
ENST00000398165	CBS-204	2605	XM_024452136	ENSP00000381231	551 (aa)	XP_024307904	P35520
ENST00000458223	CBS-208	676	-	ENSP00000408014	159 (aa)	-	H7C2W0
ENST00000470912	CBS-212	894	-	-	- (aa)	-	-
ENST00000430013	CBS-205	828	-	ENSP00000405929	224 (aa)	-	H7C2H4
ENST00000491776	CBS-216	1515	-	-	- (aa)	-	-
ENST00000488526	CBS-215	672	-	-	- (aa)	-	-
ENST00000352178	CBS-201	2583	XM_024452138	ENSP00000344460	551 (aa)	XP_024307906	P35520
ENST00000465732	CBS-211	683	-	-	- (aa)	-	-
ENST00000359624	CBS-202	2353	XM_011529774	ENSP00000352643	551 (aa)	XP_011528076	P35520
ENST00000496485	CBS-217	673	-	-	- (aa)	-	-
ENST00000398158	CBS-203	2453	XM_011529777	ENSP00000381225	551 (aa)	XP_011528079	P35520
ENST00000441030	CBS-206	819	-	ENSP00000388235	177 (aa)	-	C9JMA6

Gene Model

Click here to download ENSG00000160200's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa00260	Glycine, serine and threonine metabolism	KEGG
hsa00270	Cysteine and methionine metabolism	KEGG
hsa01100	Metabolic pathways	KEGG
hsa01230	Biosynthesis of amino acids	KEGG

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000160200	Nutritional and Metabolic Diseases	2.1730000E-006	-
ENSG00000160200	Child Development Disorders, Pervasive	3.4000000E-005	-
ENSG00000160200	Selenium	5E-6	23720494
ENSG00000160200	Homocysteine	3E-26	24651765
ENSG00000160200	Homocysteine	4E-6	23251661
ENSG00000160200	Homocysteine	3E-10	20031578
ENSG00000160200	Homocysteine	4E-24	23824729
ENSG00000160200	Selenium	5E-9	25343990
ENSG00000160200	Selenium	4E-9	25343990
ENSG00000160200	Homocysteine	2E-12	23824729
ENSG00000160200	Metabolism	1E-11	24816252
ENSG00000160200	Selenium	3E-8	25343990

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000160200	rs6586282	21	43058387	T	Blood and toenail selenium levels	25343990			EFO_0006331
ENSG00000160200	rs1789953	21	43062826	T	Blood and toenail selenium levels	25343990			EFO_0006331
ENSG00000160200	rs234709	21	43066854	T	Blood and toenail selenium levels	25343990			EFO_0006331
ENSG00000160200	rs6586282	21	43058387	?	Blood trace element (Se levels)	23720494	[0.068-0.166] unit increase	0.117	EFO_0005266
ENSG00000160200	rs234709	21	43066854	T	Homocysteine levels	23824729	[0.058-0.086] unit decrease	0.0718	EFO_0004578
ENSG00000160200	rs2851391	21	43067294	T	Homocysteine levels	23824729	[0.04-0.072] unit increase	0.056	EFO_0004578
ENSG00000160200	rs234714	21	43067923	T	Plasma homocysteine levels (post-methionine load test)	24651765	[0.31-0.49] unit increase	0.404	EFO_0004578
ENSG00000160200	rs6586282	21	43058387	?	Homocysteine levels	20031578	[NR] unit decrease	0.03	EFO_0004578
ENSG00000160200	rs2851391	21	43067294	T	Blood metabolite levels	24816252	[0.0081-0.0159] unit decrease	0.012	EFO_0005664
ENSG00000160200	rs2851391	21	43067294	G	Obesity-related traits	23251661	[NR] µmol/L increase	0.02	EFO_0004578

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000160200's network

* RBP PPI network refers to all genes directly bind to RBP

Orthologs identified by RBPome

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000160200	CBS	75	46.667	YGR155W	CYS4	85	46.667	Saccharomyces_cerevisiae

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0004122	cystathionine beta-synthase activity	7929220.18776696.19010420.22985361.23981774.24416422.	IDA	Function
GO:0004124	cysteine synthase activity	21873635.	IBA	Function
GO:0005515	protein binding	17087506.25416956.	IPI	Function
GO:0005634	nucleus	17087506.	IDA	Component
GO:0005737	cytoplasm	21873635.	IBA	Component
GO:0005737	cytoplasm	23981774.	IDA	Component
GO:0005829	cytosol	16780588.	HDA	Component
GO:0005829	cytosol	-	TAS	Component
GO:0006535	cysteine biosynthetic process from serine	21873635.	IBA	Process
GO:0006563	L-serine metabolic process	19010420.	IDA	Process
GO:0006565	L-serine catabolic process	18776696.	IDA	Process
GO:0019343	cysteine biosynthetic process via cystathionine	-	IEA	Process
GO:0019344	cysteine biosynthetic process	24416422.	IDA	Process
GO:0019346	transsulfuration	21873635.	IBA	Process
GO:0019346	transsulfuration	-	TAS	Process
GO:0019448	L-cysteine catabolic process	15520012.	IDA	Process
GO:0019825	oxygen binding	24515102.	IDA	Function
GO:0019899	enzyme binding	17087506.	IPI	Function
GO:0020037	heme binding	21873635.	IBA	Function
GO:0020037	heme binding	7929220.24515102.	IDA	Function
GO:0020037	heme binding	18776696.	IMP	Function
GO:0030170	pyridoxal phosphate binding	21873635.	IBA	Function
GO:0030170	pyridoxal phosphate binding	7929220.18776696.	IDA	Function
GO:0031625	ubiquitin protein ligase binding	17087506.	IPI	Function
GO:0042262	DNA protection	24534463.	IMP	Process
GO:0042802	identical protein binding	16189514.19447967.21900206.25416956.	IPI	Function
GO:0042803	protein homodimerization activity	11483494.	IDA	Function
GO:0043418	homocysteine catabolic process	18776696.24416422.	IDA	Process
GO:0046872	metal ion binding	-	IEA	Function
GO:0050421	nitrite reductase (NO-forming) activity	24416422.	IDA	Function
GO:0050667	homocysteine metabolic process	21873635.	IBA	Process
GO:0050667	homocysteine metabolic process	19010420.20031578.23981774.	IDA	Process
GO:0055114	oxidation-reduction process	-	IEA	Process
GO:0070025	carbon monoxide binding	24515102.	IDA	Function
GO:0070026	nitric oxide binding	24416422.24515102.	IDA	Function
GO:0070814	hydrogen sulfide biosynthetic process	21873635.	IBA	Process
GO:0070814	hydrogen sulfide biosynthetic process	15520012.24416422.	IDA	Process
GO:0070814	hydrogen sulfide biosynthetic process	-	ISS	Process
GO:0072341	modified amino acid binding	20031578.	IDA	Function
GO:1904047	S-adenosyl-L-methionine binding	22985361.	IDA	Function

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
23836652	Tumor-derived hydrogen sulfide, produced by cystathionine-β-synthase, stimulates bioenergetics, cell proliferation, and angiogenesis in colon cancer.	Proc Natl Acad Sci U S A	2013 Jul 23	Szabo C	doi: 10.1073/pnas.1306241110
23152928	Frequent epigenetic silencing of the folate-metabolising gene cystathionine-beta-synthase in gastrointestinal cancer.	PLoS One	2012	Zhao H	doi: 10.1371/journal.pone.0049683
27039165	Bioenergetic relevance of hydrogen sulfide and the interplay between gasotransmitters at human cystathionine β-synthase.	Biochim Biophys Acta	2016 Aug	Vicente JB	doi: 10.1016/j.bbabio.2016.03.030
22236648	Polymorphisms in the folate-metabolizing genes MTR, MTRR, and CBS and breast cancer risk.	Cancer Epidemiol	2012 Apr	Weiner AS	doi: 10.1016/j.canep.2011.11.010
15922487	Polymorphisms in folate metabolic genes and lung cancer risk in Xuan Wei, China.	Lung Cancer	2005 Sep	Shen M	-
26051168	Role of cystathionine β-synthase in human breast Cancer.	Free Radic Biol Med	2015 Sep	Sen S	doi: 10.1016/j.freeradbiomed.2015.05.024
24667534	Effect of S-adenosyl-L-methionine (SAM), an allosteric activator of cystathionine-β-synthase (CBS) on colorectal cancer cell proliferation and bioenergetics in vitro.	Nitric Oxide	2014 Sep 15	M??dis K	doi: 10.1016/j.niox.2014.03.001
26452259	Role of cystathionine beta synthase in lipid metabolism in ovarian cancer.	Oncotarget	2015 Nov 10	Chakraborty PK	doi: 10.18632/oncotarget.5424.
17726616	Polymorphisms in methionine synthase (A2756G) and cystathionine beta-synthase (844ins68) and susceptibility to carcinomas of the upper gastrointestinal tract.	J Cancer Res Clin Oncol	2008 Mar	Ott N	-
24236104	Cystathionine beta-synthase (CBS) contributes to advanced ovarian cancer progression and drug resistance.	PLoS One	2013 Nov 13	Bhattacharyya S	doi: 10.1371/journal.pone.0079167

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr21	43065224	Missense_Mutation	NA	E239K	0.11
CESC	chr21	43068528	Silent	rs749697783	F99F	0.67
COAD	chr21	43065234	Silent	NA	T235T	0.75
LGG	chr21	43066305	Missense_Mutation	novel	A130V	0.23
LUAD	chr21	43066280	Silent	novel	P138P	0.32
READ	chr21	43065239	Missense_Mutation	rs773734233	D234N	0.19
SKCM	chr21	43065457	Missense_Mutation	NA	S199F	0.53
SKCM	chr21	43066309	Missense_Mutation	NA	D129N	0.82
SKCM	chr21	43068562	Missense_Mutation	NA	P88L	0.62
UCEC	chr21	43066244	Splice_Region	rs750030593	T150T	0.61
UCEC	chr21	43068280	Intron	novel		0.4
UCEC	chr21	43055718	Intron	novel		0.46
UCEC	chr21	43066244	Splice_Region	rs750030593	T150T	0.21
UCEC	chr21	43065248	Missense_Mutation	novel	A231T	0.77
UCEC	chr21	43065269	Missense_Mutation	rs139456571	R224C	0.83

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
OV	DEL	0.3541	0.022578
THYM	AMP	0.0163	0.24554

Survival Analysis

Cancer	P-value	Q-value
KIRC	0.0001	Kaplan-Meier Survival Analysis
STAD	0.0059	Kaplan-Meier Survival Analysis
SARC	0.014	Kaplan-Meier Survival Analysis
MESO	0.024	Kaplan-Meier Survival Analysis
ACC	0.00095	Kaplan-Meier Survival Analysis
SKCM	0.042	Kaplan-Meier Survival Analysis
UCEC	0.0011	Kaplan-Meier Survival Analysis
LIHC	0.00017	Kaplan-Meier Survival Analysis
LGG	0.00014	Kaplan-Meier Survival Analysis
THCA	0.012	Kaplan-Meier Survival Analysis
UVM	0.0018	Kaplan-Meier Survival Analysis
OV	0.031	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Orthologs

Gene Ontology

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