Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolSHMT2
Gene nameserine hydroxymethyltransferase 2 (mitochondrial)
SynonymsGLYA|HEL-S-51e|SHMT
CytomapUCSC genome browser: 12q12-q14
Genomic locationchr12 :57624110-57628718
Type of geneprotein-coding
RefGenesNM_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 idENSG00000182199
DescriptionGLY A+epididymis secretory sperm binding protein Li 51eglycine auxotroph A, human complement for hamsterglycine hydroxymethyltransferaseserine aldolaseserine hydroxymethylaseserine hydroxymethyltransferase, mitochondrialserine methylasethreonine a
Modification date20141207
dbXrefs MIM : 138450
HGNC : HGNC
Ensembl : ENSG00000182199
HPRD : 00717
Vega : OTTHUMG00000171246
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SHMT2
BioGPS: 6472
Gene Expression Atlas: ENSG00000182199
The Human Protein Atlas: ENSG00000182199
PathwayNCI Pathway Interaction Database: SHMT2
KEGG: SHMT2
REACTOME: SHMT2
ConsensusPathDB
Pathway Commons: SHMT2
MetabolismMetaCyc: SHMT2
HUMANCyc: SHMT2
RegulationEnsembl's Regulation: ENSG00000182199
miRBase: chr12 :57,624,110-57,628,718
TargetScan: NM_001166356
cisRED: ENSG00000182199
ContextiHOP: SHMT2
cancer metabolism search in PubMed: SHMT2
UCL Cancer Institute: SHMT2
Assigned class in ccmGDBC

Top
Phenotypic Information for SHMT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SHMT2
MedGen: SHMT2 (Human Medical Genetics with Condition)
ClinVar: SHMT2
PhenotypeMGI: SHMT2 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SHMT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC009320COX8A49493116374214163744015SHMT24941567125762657657628509

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
check002.gifSNV 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

Top
check002.gifSomatic 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.

Top
check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr12:57627816-57627816p.R437H4
chr12:57627675-57627675p.G423S2
chr12:57626237-57626237p.P199L2
chr12:57626616-57626616p.R283*2
chr12:57626343-57626343p.Y234Y2
chr12:57627865-57627865p.N453N2
chr12:57628070-57628070p.R481C2
chr12:57628071-57628071p.R481L2
chr12:57626053-57626053p.E191G2
chr12:57626582-57626582p.A271A1

Top
check002.gifSNV 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 ID1234567891011121314151617181920
# sample 1 8  3 3  211  44 5
# mutation 1 8  3 3  211  45 5
nonsynonymous SNV 1 5  2 2  2 1  23 4
synonymous SNV   3  1 1   1   22 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])

Top
check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr12:57626343p.G175S,SHMT22
chr12:57626004p.G413S,SHMT22
chr12:57627675p.Y224Y,SHMT22
chr12:57628070p.R471C,SHMT21
chr12:57626334p.H269L,SHMT21
chr12:57627397p.R478L,SHMT21
chr12:57628092p.R295L,SHMT21
chr12:57627425p.R15I,SHMT21
chr12:57624596p.Y299Y,SHMT21
chr12:57626352p.A326D,SHMT21

check002.gifOther 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

check002.gifCopy 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]

Top
Gene Expression for SHMT2

check002.gifGene 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.

check002.gifDifferential 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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
Gene-Gene Network Information
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for SHMT2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00114serine hydroxymethyltransferase 2 (mitochondrial)nutraceuticalPyridoxal Phosphate
DB00116serine hydroxymethyltransferase 2 (mitochondrial)approved; nutraceuticalTetrahydrofolic acid
DB00145serine hydroxymethyltransferase 2 (mitochondrial)approved; nutraceuticalGlycine
DB00515serine hydroxymethyltransferase 2 (mitochondrial)approvedCisplatin


Top
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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas