Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 SHMT1
Basic gene info.Gene symbolSHMT1
Gene nameserine hydroxymethyltransferase 1 (soluble)
SynonymsCSHMT|SHMT
CytomapUCSC genome browser: 17p11.2
Genomic locationchr17 :18231186-18266856
Type of geneprotein-coding
RefGenesNM_001281786.1,
NM_004169.4,NM_148918.2,
Ensembl idENSG00000176974
Descriptioncytoplasmic serine hydroxymethyltransferaseglycine hydroxymethyltransferaseserine hydroxymethyltransferase, cytosolicserine methylase
Modification date20141222
dbXrefs MIM : 182144
HGNC : HGNC
Ensembl : ENSG00000176974
HPRD : 01643
Vega : OTTHUMG00000059094
ProteinUniProt: P34896
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SHMT1
BioGPS: 6470
Gene Expression Atlas: ENSG00000176974
The Human Protein Atlas: ENSG00000176974
PathwayNCI Pathway Interaction Database: SHMT1
KEGG: SHMT1
REACTOME: SHMT1
ConsensusPathDB
Pathway Commons: SHMT1
MetabolismMetaCyc: SHMT1
HUMANCyc: SHMT1
RegulationEnsembl's Regulation: ENSG00000176974
miRBase: chr17 :18,231,186-18,266,856
TargetScan: NM_001281786
cisRED: ENSG00000176974
ContextiHOP: SHMT1
cancer metabolism search in PubMed: SHMT1
UCL Cancer Institute: SHMT1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SHMT1 in cancer cell metabolism1. MacFarlane AJ, Perry CA, McEntee MF, Lin DM, Stover PJ (2011) Shmt1 heterozygosity impairs folate-dependent thymidylate synthesis capacity and modifies risk of Apcmin-mediated intestinal cancer risk. Cancer research 71: 2098-2107. go to article
2. Paone A, Marani M, Fiascarelli A, Rinaldo S, Giardina G, et al. (2014) SHMT1 knockdown induces apoptosis in lung cancer cells by causing uracil misincorporation. Cell death & disease 5: e1525. go to article

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Phenotypic Information for SHMT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SHMT1
Familial Cancer Database: SHMT1
* 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
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 182144; gene.
Orphanet
DiseaseKEGG Disease: SHMT1
MedGen: SHMT1 (Human Medical Genetics with Condition)
ClinVar: SHMT1
PhenotypeMGI: SHMT1 (International Mouse Phenotyping Consortium)
PhenomicDB: SHMT1

Mutations for SHMT1
* 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 SHMT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF356130TFCP2L1453212122041465122041739SHMT1309382171823838418238457
AX747021SHMT112757171823399718236753MLLT11275330881151040932151041267
BF356132TFCP2L193232122041420122041739SHMT1311384171823838418238457
AK091498SHMT112757171823399718236753MLLT11275330881151040932151041267

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

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2                
GAIN (# sample)2                
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr17:18259194-18259194p.?2
chr17:18243507-18243507p.G222R2
chr17:18232096-18232096p.L474F2
chr17:18232688-18232688p.L396V2
chr17:18250892-18250892p.G146V2
chr17:18250897-18250897p.P144P2
chr17:18232670-18232670p.R402W1
chr17:18243490-18243490p.A227A1
chr17:18232093-18232093p.F475V1
chr17:18250958-18250958p.N124I1

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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
# sample1114  2 1  322  2315
# mutation1114  2 1  322  2315
nonsynonymous SNV1 12  1 1  2 2  12 4
synonymous SNV 1 2  1    12   1111
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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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
chr17:18232688p.G8E,SHMT12
chr17:18250892p.L258V,SHMT12
chr17:18233940p.F337V,SHMT11
chr17:18250897p.A74V,SHMT11
chr17:18232093p.A321A,SHMT11
chr17:18233941p.R69L,SHMT11
chr17:18250933p.A321V,SHMT11
chr17:18232139p.R53C,SHMT11
chr17:18233963p.D300N,SHMT11
chr17:18250958p.G8G,SHMT11

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 SHMT1 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 SHMT1

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))
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check002.gifCNV 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
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

ALKBH5,ATPAF2,B9D1,GID4,COPS3,DRG2,DVL2,
EVPLL,FLII,LLGL1,MAPK7,MED9,OR5M3,PIGL,
PRPSAP2,SFXN2,SHMT1,MIEF2,SMYD4,TOP3A,ZSWIM7
ACACB,ALDH1L1,ASS1,C17orf53,C20orf27,CIDEA,CKB,
CYB5A,ECHDC3,GLUL,HADH,HRSP12,MLXIPL,MOCS1,
ORMDL3,PC,SHMT1,SLC25A1,STAT5A,TM7SF2,TMEM120A

ATPAF2,AURKB,C1QBP,COPS3,COX10,ECHS1,EIF4A1,
EIF5A,EIF5AL1,ELAC2,FAM64A,GLOD4,MPDU1,PFN1,
RNMTL1,SCO1,SHMT1,SLC25A11,TTC19,WRAP53,YWHAE
AKR1A1,DNPH1,C9orf41,CA9,CDCA3,DDC,DHRS4L2,
EPHA1,ESPL1,FAH,FANCC,GCHFR,LCLAT1,MOCOS,
NPY6R,OTC,PCYT2,PNPO,SHMT1,SLC25A15,SLC2A9
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

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check002.gifInteracting 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 SHMT1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P34896; -.
ChemistryChEMBL CHEMBL1772927; -.
Organism-specific databasesPharmGKB PA35753; -.
Organism-specific databasesCTD 6470; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00114serine hydroxymethyltransferase 1 (soluble)nutraceuticalPyridoxal Phosphate
DB00116serine hydroxymethyltransferase 1 (soluble)approved; nutraceuticalTetrahydrofolic acid
DB00145serine hydroxymethyltransferase 1 (soluble)approved; nutraceuticalGlycine
DB01055serine hydroxymethyltransferase 1 (soluble)approvedMimosine
DB02067serine hydroxymethyltransferase 1 (soluble)experimentalTriglu-5-Formyl-Tetrahydrofolate
DB02800serine hydroxymethyltransferase 1 (soluble)experimental5-Hydroxymethylene-6-Hydrofolic Acid
DB02824serine hydroxymethyltransferase 1 (soluble)experimentalN-Pyridoxyl-Glycine-5-Monophosphate
DB00515serine hydroxymethyltransferase 1 (soluble)approvedCisplatin
DB00531serine hydroxymethyltransferase 1 (soluble)approved; investigationalCyclophosphamide
DB00970serine hydroxymethyltransferase 1 (soluble)approvedDactinomycin
DB00997serine hydroxymethyltransferase 1 (soluble)approved; investigationalDoxorubicin
DB00541serine hydroxymethyltransferase 1 (soluble)approved; investigationalVincristine
DB00133serine hydroxymethyltransferase 1 (soluble)approved; nutraceuticalL-Serine
DB00563serine hydroxymethyltransferase 1 (soluble)approvedMethotrexate
DB00115serine hydroxymethyltransferase 1 (soluble)approved; nutraceuticalCyanocobalamin
DB00158serine hydroxymethyltransferase 1 (soluble)approved; nutraceuticalFolic Acid


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Cross referenced IDs for SHMT1
* 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



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