Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	Gene Summary
	Phenotypic Information (metabolism pathway, cancer, disease, phenome)
	Mutations : SVs, CNVs, SNVs
	Gene expression: GE, Protein, DEGE, CNV vs GE
	Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG
	Pharmacological Information: Drug-Gene Network
	Cross referenced IDs

Gene Summary for SHMT2

Basic gene info.	Gene symbol	SHMT2
	Gene name	serine hydroxymethyltransferase 2 (mitochondrial)
	Synonyms	GLYA\|HEL-S-51e\|SHMT
	Cytomap	UCSC genome browser: 12q12-q14
	Genomic location	chr12 :57624110-57628718
	Type of gene	protein-coding
	RefGenes	NM_001166356.1, NM_001166357.1,NM_001166358.1,NM_001166359.1,NM_005412.5, NR_029415.1,NR_029416.1,NR_029417.1,NR_048562.1,
	Ensembl id	ENSG00000182199
	Description	GLY A+epididymis secretory sperm binding protein Li 51eglycine auxotroph A, human complement for hamsterglycine hydroxymethyltransferaseserine aldolaseserine hydroxymethylaseserine hydroxymethyltransferase, mitochondrialserine methylasethreonine a
	Modification date	20141207
dbXrefs	MIM : 138450
	HGNC : HGNC
	Ensembl : ENSG00000182199
	HPRD : 00717
	Vega : OTTHUMG00000171246
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SHMT2
	BioGPS: 6472
	Gene Expression Atlas: ENSG00000182199
	The Human Protein Atlas: ENSG00000182199
Pathway	NCI Pathway Interaction Database: SHMT2
	KEGG: SHMT2
	REACTOME: SHMT2
	ConsensusPathDB
	Pathway Commons: SHMT2
Metabolism	MetaCyc: SHMT2
	HUMANCyc: SHMT2
Regulation	Ensembl's Regulation: ENSG00000182199
	miRBase: chr12 :57,624,110-57,628,718
	TargetScan: NM_001166356
	cisRED: ENSG00000182199
Context	iHOP: SHMT2
	cancer metabolism search in PubMed: SHMT2
	UCL Cancer Institute: SHMT2
Assigned class in ccmGDB	C

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Phenotypic Information for SHMT2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SHMT2
	Familial Cancer Database: SHMT2

* This gene is included in those cancer gene databases.


Oncogene ¹	Tumor Suppressor gene ²	Cancer Gene Census ³	CancerGenes ⁴	Network of Cancer Gene ⁵	Significant driver gene in	Therapeutic Vulnerabilities in Cancer¹

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: SHMT2
	MedGen: SHMT2 (Human Medical Genetics with Condition)
	ClinVar: SHMT2
Phenotype	MGI: SHMT2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SHMT2

Mutations for SHMT2

* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SHMT2 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

BC009320

COX8A

493

63742141

63744015

SHMT2

494

1567

57626576

57628509

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

There's no copy number variation information in COSMIC data for this gene.

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SNV Counts per Each Loci in COSMIC data : go to COSMIC point mutation

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=32)	Stat. for Synonymous SNVs (# total SNVs=12)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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Top 10 SNVs Having the Most Samples in COSMIC data

* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.

GRCh37 position	Mutation(aa)	Unique sampleID count
chr12:57627816-57627816	p.R437H	4
chr12:57627675-57627675	p.G423S	2
chr12:57626237-57626237	p.P199L	2
chr12:57626616-57626616	p.R283*	2
chr12:57626343-57626343	p.Y234Y	2
chr12:57627865-57627865	p.N453N	2
chr12:57628070-57628070	p.R481C	2
chr12:57628071-57628071	p.R481L	2
chr12:57626053-57626053	p.E191G	2
chr12:57626582-57626582	p.A271A	1

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		1		8			3		3			2	1	1			4	4		5
# mutation		1		8			3		3			2	1	1			4	5		5
nonsynonymous SNV		1		5			2		2			2		1			2	3		4
synonymous SNV				3			1		1				1				2	2		1

cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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Top 10 SNVs Having the Most Samples in TCGA data

* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.

Genomic Position	Mutation(aa)	Unique sampleID count
chr12:57626343	p.G175S,SHMT2	2
chr12:57626004	p.G413S,SHMT2	2
chr12:57627675	p.Y224Y,SHMT2	2
chr12:57628070	p.R471C,SHMT2	1
chr12:57626334	p.H269L,SHMT2	1
chr12:57627397	p.R478L,SHMT2	1
chr12:57628092	p.R295L,SHMT2	1
chr12:57627425	p.R15I,SHMT2	1
chr12:57624596	p.Y299Y,SHMT2	1
chr12:57626352	p.A326D,SHMT2	1

Other DBs for Point Mutations

Point Mutation Table of Ensembl: go to Ensembl variation table

Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

Copy Number for SHMT2 in TCGA

* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.

cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for SHMT2

Gene Expression in Cancer Cell-lines (CCLE)

* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

Differential Gene Expression in Primary Tumors (TCGA)

* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-Expressed gene's network Plot

* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types


AURKB,CCT7,CDT1,EIF2S2,FAM64A,GAPDH,LMNB2, MARS,NXPH4,PLK1,RAN,RANBP1,SHMT2,TPI1, TROAP,TUBA1B,TUBA1C,UQCRH,UQCRHL,WDR4,YARS	AHCY,ALKBH2,C19orf48,SAPCD2,CCT3,DEAF1,EIF3B, ERGIC3,EXOSC5,H2AFY2,IMPDH2,IPO4,NIPSNAP1,NPM3, PIK3R2,PYCR1,QARS,LEPREL4,SHMT2,SMARCA4,SMARCD2

AAAS,ATP5B,CENPM,CHAF1B,DDX54,GAPDH,GOT1, HSP90B1,PA2G4,PCBP2,PGAM5,PSMD9,RAN,RFC5, SRSF9,SHMT2,SLC25A3,TIMELESS,TPI1,TSFM,TUBA1B	AURKB,CCNB2,CDC20,CDCA5,CDCA8,CDT1,FANCG, HJURP,KIF18A,KIF2C,MCM2,NUSAP1,PLK1,PTDSS1, PTTG1,SHMT2,SSRP1,TK1,TRAIP,TRAP1,UBE2C

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for SHMT2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00114	serine hydroxymethyltransferase 2 (mitochondrial)	nutraceutical	Pyridoxal Phosphate
DB00116	serine hydroxymethyltransferase 2 (mitochondrial)	approved; nutraceutical	Tetrahydrofolic acid
DB00145	serine hydroxymethyltransferase 2 (mitochondrial)	approved; nutraceutical	Glycine
DB00515	serine hydroxymethyltransferase 2 (mitochondrial)	approved	Cisplatin

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Cross referenced IDs for SHMT2

* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information