EuRBPDB

Note: to get the extension of tumor abbreviations.

Cancer Related Information
Basic Information

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
26975021	Metabolic phenotype of bladder cancer.	Cancer Treat Rev	2016 Apr	Massari F	doi: 10.1016/j.ctrv.2016.03.005
27666119	Prognostic and therapeutic value of mitochondrial serine hydroxyl-methyltransferase 2 as a breast cancer biomarker.	Oncol Rep	2016 Nov	Zhang L	doi: 10.3892/or.2016.5112
29020998	Proteomic profiling of breast cancer metabolism identifies SHMT2 and ASCT2 as prognostic factors.	Breast Cancer Res	2017 Oct 11	Bernhardt S	doi: 10.1186/s13058-017-0905-7.
29180469	SHMT2 Desuccinylation by SIRT5 Drives Cancer Cell Proliferation.	Cancer Res	2018 Jan 15	Yang X	doi: 10.1158/0008-5472.CAN-17-1912
30367038	Deacetylation of serine hydroxymethyl-transferase 2 by SIRT3 promotes colorectal carcinogenesis.	Nat Commun	2018 Oct 26	Wei Z	doi: 10.1038/s41467-018-06812-y.

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr12	57231558	Splice_Region	novel	K103K	0.33
BLCA	chr12	57230996	Nonsense_Mutation	novel	S76*	0.29
BLCA	chr12	57232781	Silent	novel	P265P	0.47
BLCA	chr12	57234421	3'UTR	novel		0.18
BLCA	chr12	57233820	Missense_Mutation	novel	V399M	0.37
BRCA	chr12	57232800	Missense_Mutation	NA	D272N	0.13
BRCA	chr12	57232785	Missense_Mutation	novel	P267A	0.13
BRCA	chr12	57229778	5'UTR	novel		0.11
BRCA	chr12	57232569	Missense_Mutation	NA	M237I	0.51
BRCA	chr12	57232751	Silent	rs768724092	I255I	0.46
BRCA	chr12	57232456	Frame_Shift_Del	NA	*T201Lfs11**	0.38
CESC	chr12	57234301	Silent	NA	L485L	0.08
CESC	chr12	57233660	Nonsense_Mutation	novel	S374*	0.19
CESC	chr12	57231729	Missense_Mutation	NA	E110Q	0.2
COAD	chr12	57232449	Splice_Region	rs767579674		0.2
COAD	chr12	57233614	Missense_Mutation	NA	R359W	0.42
COAD	chr12	57233329	Missense_Mutation	novel	A336D	0.18
COAD	chr12	57232560	Silent	rs561041442	Y234Y	0.22
COAD	chr12	57232221	Missense_Mutation	novel	G175S	0.41
COAD	chr12	57232763	Silent	rs781224640	V259V	0.43
COAD	chr12	57231508	Missense_Mutation	rs373156028	A87T	0.37
COAD	chr12	57234368	3'UTR	novel		0.08
COAD	chr12	57233300	Frame_Shift_Del	novel	*H328Tfs8**	0.54
ESCA	chr12	57234101	Missense_Mutation	novel	S460G	0.26
ESCA	chr12	57233267	Silent	novel	I315I	0.2
GBM	chr12	57234021	Missense_Mutation	novel	S433Y	0.19
GBM	chr12	57234525	3'UTR	novel		0.29
GBM	chr12	57232548	Silent	novel	R230R	0.06
GBM	chr12	57232818	Missense_Mutation	novel	T278S	0.07
HNSC	chr12	57232262	Missense_Mutation	novel	I188M	0.22
HNSC	chr12	57232775	Silent	novel	V263V	0.23
HNSC	chr12	57234401	3'UTR	novel		0.32
HNSC	chr12	57232551	Silent	novel	L231L	0.33
HNSC	chr12	57233642	Missense_Mutation	rs776714754	R368Q	0.16
KIRC	chr12	57233826	Missense_Mutation	novel	E401K	0.2
KIRC	chr12	57232283	Frame_Shift_Del	novel	Y195*	0.33
KIRP	chr12	57230866	Missense_Mutation	NA	Q33E	0.41
KIRP	chr12	57231894	Missense_Mutation	NA	D165H	0.19
LGG	chr12	57233249	Silent	novel	Y309Y	0.24
LIHC	chr12	57231486	Missense_Mutation	NA	F79L	0.56
LIHC	chr12	57233620	Missense_Mutation	novel	M361V	0.12
LUAD	chr12	57233785	Missense_Mutation	novel	R387L	0.1
LUAD	chr12	57233197	Missense_Mutation	novel	Y292F	0.09
LUAD	chr12	57233236	Missense_Mutation	NA	R305L	0.2
LUSC	chr12	57232518	Silent	NA	L220L	0.14
LUSC	chr12	57231752	Silent	rs745814583	L117L	0.37
OV	chr12	57234347	Missense_Mutation	novel	F501V	0.12
OV	chr12	57234348	Frame_Shift_Ins	novel	*D502Cfs33**	0.12
OV	chr12	57234017	Missense_Mutation	novel	T432S	0.05
OV	chr12	57233614	Missense_Mutation	NA	R359W	0.29
OV	chr12	57234507	3'UTR	novel		0.09
OV	chr12	57232529	In_Frame_Del	novel	T225_R236del	0.26
OV	chr12	57234056	Missense_Mutation	novel	V445M	0.06
OV	chr12	57234026	Nonsense_Mutation	novel	Q435*	0.08
OV	chr12	57234399	3'UTR	novel		0.4
PAAD	chr12	57231846	Missense_Mutation	novel	A149T	0.16
PAAD	chr12	57232499	Missense_Mutation	rs199498720	R214Q	0.19
PAAD	chr12	57232575	Missense_Mutation	novel	E239D	0.17
PRAD	chr12	57234454	3'UTR	novel		0.67
PRAD	chr12	57232454	Missense_Mutation	NA	P199L	0.29
READ	chr12	57232477	Missense_Mutation	novel	N207H	0.18
READ	chr12	57232268	Silent	novel	F190F	0.48
SARC	chr12	57232755	Missense_Mutation	novel	G257S	0.09
SARC	chr12	57233828	Missense_Mutation	novel	E401D	0.13
SARC	chr12	57234288	Missense_Mutation	rs536394351	R481H	0.04
SKCM	chr12	57232507	Missense_Mutation	rs747827761	R217W	0.46
SKCM	chr12	57233571	Silent	NA	T344T	0.22
SKCM	chr12	57232454	Missense_Mutation	NA	P199L	0.46
SKCM	chr12	57234294	Missense_Mutation	novel	A483V	0.15
SKCM	chr12	57234295	Silent	novel	A483A	0.14
SKCM	chr12	57232800	Missense_Mutation	NA	D272N	0.04
SKCM	chr12	57234031	Silent	NA	F436F	0.37
STAD	chr12	57233294	Frame_Shift_Del	rs778420323	*G326Afs10**	0.27
STAD	chr12	57233844	Missense_Mutation	novel	A407T	0.16
STAD	chr12	57234284	Nonsense_Mutation	NA	Q480*	0.35
STAD	chr12	57233300	Frame_Shift_Del	novel	*H328Tfs8**	0.21
STAD	chr12	57232293	Splice_Site	rs778184704	X198_splice	0.44
STAD	chr12	57232560	Silent	rs561041442	Y234Y	0.14
STAD	chr12	57233300	Frame_Shift_Del	novel	*H328Tfs8**	0.18
STAD	chr12	57233808	Missense_Mutation	rs369332082	R395W	0.11
STAD	chr12	57233892	Missense_Mutation	rs751223752	G423S	0.24
STAD	chr12	57231561	Splice_Site	NA	X104_splice	0.36
STAD	chr12	57232801	Missense_Mutation	novel	D272G	0.29
STAD	chr12	57232514	Missense_Mutation	novel	R219L	0.15
STAD	chr12	57233294	Frame_Shift_Del	rs778420323	*G326Afs10**	0.16
STAD	chr12	57232833	Nonsense_Mutation	rs758199349	R283*	0.12
STAD	chr12	57233233	Missense_Mutation	novel	G304D	0.38
UCEC	chr12	57230813	Missense_Mutation	NA	R15I	0.37
UCEC	chr12	57232833	Nonsense_Mutation	rs758199349	R283*	0.33
UCEC	chr12	57230653	Intron	novel		0.12
UCEC	chr12	57230813	Missense_Mutation	NA	R15I	0.18
UCEC	chr12	57231914	Splice_Site	novel	X171_splice	0.63
UCEC	chr12	57234094	Silent	NA	E457E	0.19
UCEC	chr12	57231768	Missense_Mutation	NA	A123T	0.53
UCEC	chr12	57233809	Missense_Mutation	novel	R395Q	0.5
UCEC	chr12	57234549	3'UTR	novel		0.5
UCEC	chr12	57232797	Missense_Mutation	rs760592358	A271T	0.42
UCEC	chr12	57233583	Silent	novel	R348R	0.16
UCEC	chr12	57231736	Missense_Mutation	novel	V112A	0.43
UCEC	chr12	57234309	Missense_Mutation	rs200906224	R488Q	0.39
UCEC	chr12	57230812	Silent	novel	R15R	0.34
UCEC	chr12	57233892	Missense_Mutation	rs751223752	G423S	0.41
UCEC	chr12	57230602	Intron	novel		0.16
UCEC	chr12	57234287	Missense_Mutation	rs766431147	R481C	0.34
UCEC	chr12	57231903	Missense_Mutation	novel	D168N	0.29
UCEC	chr12	57232458	Missense_Mutation	novel	K200N	0.24
UCEC	chr12	57233314	Missense_Mutation	novel	A331V	0.16
UCEC	chr12	57233641	Nonsense_Mutation	rs369589054	R368*	0.49
UCEC	chr12	57234023	Nonsense_Mutation	rs759124152	R434*	0.17
UCEC	chr12	57234477	3'UTR	rs185235043		0.22

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
ACC	DEL	0.0333	0.20414
DLBC	AMP	0.2083	0.085003
PCPG	AMP	0.0926	0.028953
READ	DEL	0.0667	0.064633

Survival Analysis

Cancer	P-value	Q-value
SARC	0.00059	Kaplan-Meier Survival Analysis
MESO	0.0015	Kaplan-Meier Survival Analysis
ACC	0.00011	Kaplan-Meier Survival Analysis
SKCM	0.0064	Kaplan-Meier Survival Analysis
PRAD	0.029	Kaplan-Meier Survival Analysis
BRCA	0.0021	Kaplan-Meier Survival Analysis
KIRP	0.0021	Kaplan-Meier Survival Analysis
KICH	0.029	Kaplan-Meier Survival Analysis
UCEC	0.022	Kaplan-Meier Survival Analysis
LIHC	0.02	Kaplan-Meier Survival Analysis
LGG	0.0086	Kaplan-Meier Survival Analysis
CHOL	0.014	Kaplan-Meier Survival Analysis
LUAD	0.029	Kaplan-Meier Survival Analysis
OV	0.026	Kaplan-Meier Survival Analysis

Drugs

Cell lines and drugs in GSE70138 or GSE92742

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

Pathways

Phenotypes

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000182199 (Gene tree)
Gene ID: 6472
Gene Symbol: SHMT2
Alias: SHMT
Full Name: serine hydroxymethyltransferase 2
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 5,609 bases
Position: chr12:57,229,327-57,234,935
Accession: 10852
RBP type: non-canonical RBP
Summary: This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & HEK293	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & MCF10A	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
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
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & U2OS	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
30809670	The moonlighting RNA-binding activity of cytosolic serine hydroxymethyltransferase contributes to control compartmentalization of serine metabolism.	Nucleic Acids Res	2019 May 7	Guiducci G	doi: 10.1093/nar/gkz129.
30755591	Long noncoding RNA LINC01234 promotes serine hydroxymethyltransferase 2 expression and proliferation by competitively binding miR-642a-5p in colon cancer.	Cell Death Dis	2019 Feb 12	Lin C	doi: 10.1038/s41419-019-1352-4.

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000554975	SHMT2-216	780	-	ENSP00000452404	215 (aa)	-	G3V5L0
ENST00000553868	SHMT2-208	941	-	-	- (aa)	-	-
ENST00000557487	SHMT2-232	1918	-	ENSP00000452315	494 (aa)	-	P34897
ENST00000556737	SHMT2-224	572	-	ENSP00000451495	147 (aa)	-	G3V3Y8
ENST00000553950	SHMT2-210	584	-	-	- (aa)	-	-
ENST00000556689	SHMT2-223	768	-	ENSP00000452035	237 (aa)	-	G3V4W5
ENST00000555213	SHMT2-218	611	-	-	- (aa)	-	-
ENST00000557302	SHMT2-228	457	-	-	- (aa)	-	-
ENST00000554656	SHMT2-215	817	-	-	- (aa)	-	-
ENST00000557740	SHMT2-235	569	-	-	- (aa)	-	-
ENST00000554467	SHMT2-212	3416	-	-	- (aa)	-	-
ENST00000557269	SHMT2-227	576	-	ENSP00000450594	52 (aa)	-	G3V2D2
ENST00000557348	SHMT2-229	1659	-	ENSP00000450927	65 (aa)	-	G3V2Y1
ENST00000449049	SHMT2-203	2121	-	ENSP00000413770	483 (aa)	-	P34897
ENST00000555563	SHMT2-219	895	-	ENSP00000451630	86 (aa)	-	G3V3C6
ENST00000554310	SHMT2-211	579	-	ENSP00000450893	160 (aa)	-	G3V2W0
ENST00000556798	SHMT2-225	525	-	-	- (aa)	-	-
ENST00000553474	SHMT2-205	1765	-	ENSP00000452419	483 (aa)	-	P34897
ENST00000557427	SHMT2-230	569	-	ENSP00000452045	159 (aa)	-	G3V4X0
ENST00000553324	SHMT2-204	566	-	-	- (aa)	-	-
ENST00000557529	SHMT2-233	1369	-	ENSP00000450490	264 (aa)	-	H0YIZ0
ENST00000328923	SHMT2-201	2537	-	ENSP00000333667	504 (aa)	-	P34897
ENST00000554600	SHMT2-213	837	-	-	- (aa)	-	-
ENST00000555116	SHMT2-217	1885	-	ENSP00000452339	65 (aa)	-	G3V2Y1
ENST00000554604	SHMT2-214	879	-	ENSP00000452163	192 (aa)	-	G3V540
ENST00000556825	SHMT2-226	2215	-	ENSP00000451169	86 (aa)	-	G3V3C6
ENST00000557703	SHMT2-234	542	-	ENSP00000450452	142 (aa)	-	G3V241
ENST00000555634	SHMT2-220	964	-	ENSP00000450930	234 (aa)	-	G3V2Y4
ENST00000553949	SHMT2-209	552	-	-	- (aa)	-	-
ENST00000557433	SHMT2-231	1904	-	ENSP00000450610	171 (aa)	-	G3V2E4
ENST00000553837	SHMT2-207	2152	-	ENSP00000451371	192 (aa)	-	G3V540
ENST00000553529	SHMT2-206	562	-	ENSP00000452161	147 (aa)	-	G3V3Y8
ENST00000555774	SHMT2-222	2311	-	ENSP00000451872	65 (aa)	-	G3V2Y1
ENST00000414700	SHMT2-202	2006	XM_011538675	ENSP00000406881	483 (aa)	XP_011536977	P34897
ENST00000555773	SHMT2-221	600	-	ENSP00000451968	149 (aa)	-	G3V4T0

Gene Model

Click here to download ENSG00000182199's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa00260	Glycine, serine and threonine metabolism	KEGG
hsa00630	Glyoxylate and dicarboxylate metabolism	KEGG
hsa00670	One carbon pool by folate	KEGG
hsa01100	Metabolic pathways	KEGG
hsa01200	Carbon metabolism	KEGG
hsa01230	Biosynthesis of amino acids	KEGG
hsa01523	Antifolate resistance	KEGG

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000182199	Schizophrenia	1E-11	26198764
ENSG00000182199	Schizophrenia	2E-12	25056061

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000182199'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
ENSG00000182199	SHMT2	100	64.530	FBgn0029823	Shmt	98	60.131	Drosophila_melanogaster
ENSG00000182199	SHMT2	100	95.814	ENSMUSG00000025403	Shmt2	99	94.036	Mus_musculus
ENSG00000182199	SHMT2	100	63.248	YLR058C	SHM2	96	55.727	Saccharomyces_cerevisiae

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0002082	regulation of oxidative phosphorylation	21873635.	IBA	Process
GO:0002082	regulation of oxidative phosphorylation	29364879.29452640.	IMP	Process
GO:0003682	chromatin binding	18063578.	IDA	Function
GO:0004372	glycine hydroxymethyltransferase activity	21873635.	IBA	Function
GO:0004372	glycine hydroxymethyltransferase activity	8505317.17482557.24075985.25619277.29180469.29364879.29452640.	IDA	Function
GO:0005515	protein binding	25416956.25902260.26871637.	IPI	Function
GO:0005634	nucleus	24075985.	IDA	Component
GO:0005737	cytoplasm	24075985.	IDA	Component
GO:0005739	mitochondrion	21873635.	IBA	Component
GO:0005739	mitochondrion	17482557.24075985.	IDA	Component
GO:0005743	mitochondrial inner membrane	21873635.	IBA	Component
GO:0005743	mitochondrial inner membrane	21876188.	IDA	Component
GO:0005743	mitochondrial inner membrane	-	TAS	Component
GO:0005758	mitochondrial intermembrane space	-	IEA	Component
GO:0005759	mitochondrial matrix	21873635.	IBA	Component
GO:0005759	mitochondrial matrix	11516159.21876188.	IDA	Component
GO:0006544	glycine metabolic process	21873635.	IBA	Process
GO:0006544	glycine metabolic process	25619277.29180469.	IDA	Process
GO:0006563	L-serine metabolic process	25619277.29180469.	IDA	Process
GO:0006564	L-serine biosynthetic process	-	IEA	Process
GO:0006565	L-serine catabolic process	21873635.	IBA	Process
GO:0006730	one-carbon metabolic process	21873635.	IBA	Process
GO:0006730	one-carbon metabolic process	11516159.29180469.29364879.29452640.	IDA	Process
GO:0008270	zinc ion binding	21873635.	IBA	Function
GO:0008284	positive regulation of cell proliferation	-	IEA	Process
GO:0008732	L-allo-threonine aldolase activity	-	IEA	Function
GO:0015630	microtubule cytoskeleton	-	IDA	Component
GO:0016597	amino acid binding	21873635.	IBA	Function
GO:0019264	glycine biosynthetic process from serine	21873635.	IBA	Process
GO:0030170	pyridoxal phosphate binding	21873635.	IBA	Function
GO:0030170	pyridoxal phosphate binding	25619277.	IDA	Function
GO:0034340	response to type I interferon	21873635.	IBA	Process
GO:0034340	response to type I interferon	24075985.	IDA	Process
GO:0035999	tetrahydrofolate interconversion	-	IEA	Process
GO:0042645	mitochondrial nucleoid	18063578.	IDA	Component
GO:0042802	identical protein binding	21873635.	IBA	Function
GO:0046653	tetrahydrofolate metabolic process	21873635.	IBA	Process
GO:0046653	tetrahydrofolate metabolic process	24075985.25619277.	IDA	Process
GO:0046655	folic acid metabolic process	21873635.	IBA	Process
GO:0046655	folic acid metabolic process	-	TAS	Process
GO:0050897	cobalt ion binding	21873635.	IBA	Function
GO:0051262	protein tetramerization	25619277.	IDA	Process
GO:0051289	protein homotetramerization	21873635.	IBA	Process
GO:0051289	protein homotetramerization	29180469.	IDA	Process
GO:0070062	extracellular exosome	19056867.20458337.	HDA	Component
GO:0070129	regulation of mitochondrial translation	29364879.29452640.	IMP	Process
GO:0070536	protein K63-linked deubiquitination	24075985.	IMP	Process
GO:0070552	BRISC complex	21873635.	IBA	Component
GO:0070552	BRISC complex	24075985.	IDA	Component
GO:0070905	serine binding	21873635.	IBA	Function
GO:1903715	regulation of aerobic respiration	29364879.29452640.	IMP	Process
GO:1904482	cellular response to tetrahydrofolate	21873635.	IBA	Process

EuRBPDB

Note: to get the extension of tumor abbreviations.

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

Pathways

Phenotypes

PPI

Orthologs

Gene Ontology

Note: Click here to get the extension of tumor abbreviations.

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742

Note: to get the extension of tumor abbreviations.