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 SLC22A2
Basic gene info.Gene symbolSLC22A2
Gene namesolute carrier family 22 (organic cation transporter), member 2
SynonymsOCT2
CytomapUCSC genome browser: 6q25.3
Genomic locationchr6 :160637793-160679963
Type of geneprotein-coding
RefGenesNM_003058.3,
NM_153191.1,
Ensembl idENSG00000112499
Descriptionorganic cation transporter 2solute carrier family 22 member 2
Modification date20141222
dbXrefs MIM : 602608
HGNC : HGNC
Ensembl : ENSG00000112499
HPRD : 04008
Vega : OTTHUMG00000015950
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC22A2
BioGPS: 6582
Gene Expression Atlas: ENSG00000112499
The Human Protein Atlas: ENSG00000112499
PathwayNCI Pathway Interaction Database: SLC22A2
KEGG: SLC22A2
REACTOME: SLC22A2
ConsensusPathDB
Pathway Commons: SLC22A2
MetabolismMetaCyc: SLC22A2
HUMANCyc: SLC22A2
RegulationEnsembl's Regulation: ENSG00000112499
miRBase: chr6 :160,637,793-160,679,963
TargetScan: NM_003058
cisRED: ENSG00000112499
ContextiHOP: SLC22A2
cancer metabolism search in PubMed: SLC22A2
UCL Cancer Institute: SLC22A2
Assigned class in ccmGDBC

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Phenotypic Information for SLC22A2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC22A2
Familial Cancer Database: SLC22A2
* 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
REACTOME_ABACAVIR_TRANSPORT_AND_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC22A2
MedGen: SLC22A2 (Human Medical Genetics with Condition)
ClinVar: SLC22A2
PhenotypeMGI: SLC22A2 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC22A2

Mutations for SLC22A2
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasSLC22A2chr6160641959160641979chr6119680562119680582
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SLC22A2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=54)
Stat. for Synonymous SNVs
(# total SNVs=32)
Stat. for Deletions
(# total SNVs=2)
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
chr6:160671634-160671634p.R207C4
chr6:160679569-160679569p.T74M3
chr6:160662608-160662608p.V467I3
chr6:160679775-160679775p.V5V3
chr6:160668235-160668235p.S313Y2
chr6:160679619-160679619p.A57A2
chr6:160679400-160679400p.T130T2
chr6:160679514-160679514p.Y92Y2
chr6:160664675-160664675p.R403H2
chr6:160679627-160679627p.G55R2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 54 4 11 961  196114
# mutation11 54 4 11 961  226120
nonsynonymous SNV 1 43 3 11 341  134 6
synonymous SNV1  11 1    62   92114
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
chr6:160679775p.V5V3
chr6:160664675p.A57A2
chr6:160679619p.Y92Y2
chr6:160679514p.R403H2
chr6:160679695p.I167I1
chr6:160662605p.P86P1
chr6:160670411p.R534I1
chr6:160664743p.R403C1
chr6:160679385p.A316S1
chr6:160679532p.F161L1

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 SLC22A2 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 SLC22A2

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

CALCA,CRLF1,CRTAC1,CYSLTR2,FILIP1,GPR133,GUCY2GP,
IL15,IRF4,LOC154822,MAPK4,PDE3A,PLA2G2A,PLA2G4A,
PPARGC1A,SLAIN1,SLC22A2,SLC22A3,USH1C,VAT1L,WNT1
VRTN,C1QTNF8,C7orf33,CLPS,COL9A1,CPNE6,DKFZP434H168,
DRP2,HBG2,HTR1B,ITIH3,ITLN1,KIF1A,MLC1,
NKX2-3,NOBOX,P2RX1,SLC22A2,SOST,WFDC1,ZFP42

AIPL1,CARD17,CLIC2,CT62,CXorf30,ENHO,FAM131B,
FAM178B,IL12RB1,ILDR2,KCNC4,LOC645431,MYH6,OR52N2,
OR7C2,PSG10P,RAB9B,RAET1E,RBP4,SLC22A2,TAS2R7
C20orf166-AS1,C9orf9,CC2D2A,CTF1,DPP6,ESYT3,FAM129A,
FBXL22,FXYD6,COLGALT2,KANK2,KLHDC8B,MAB21L2,MAP6,
NPHP1,NPTX1,SLC22A2,STAC,TCEAL2,TUBG2,WDR17
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 SLC22A2
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
DB00331solute carrier family 22 (organic cation transporter), member 2approvedMetformin
DB00690solute carrier family 22 (organic cation transporter), member 2illicit; approvedFlurazepam
DB00988solute carrier family 22 (organic cation transporter), member 2approvedDopamine
DB00126solute carrier family 22 (organic cation transporter), member 2approved; nutraceuticalVitamin C
DB00122solute carrier family 22 (organic cation transporter), member 2approved; nutraceuticalCholine
DB00501solute carrier family 22 (organic cation transporter), member 2approvedCimetidine
DB00958solute carrier family 22 (organic cation transporter), member 2approvedCarboplatin
DB00515solute carrier family 22 (organic cation transporter), member 2approvedCisplatin
DB00526solute carrier family 22 (organic cation transporter), member 2approved; investigationalOxaliplatin
DB01273solute carrier family 22 (organic cation transporter), member 2approved; investigationalVarenicline
DB00879solute carrier family 22 (organic cation transporter), member 2approved; investigationalEmtricitabine
DB00709solute carrier family 22 (organic cation transporter), member 2approved; investigationalLamivudine
DB00495solute carrier family 22 (organic cation transporter), member 2approvedZidovudine


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Cross referenced IDs for SLC22A2
* 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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