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 SLC10A2
Basic gene info.Gene symbolSLC10A2
Gene namesolute carrier family 10 (sodium/bile acid cotransporter), member 2
SynonymsASBT|IBAT|ISBT|NTCP2|PBAM
CytomapUCSC genome browser: 13q33
Genomic locationchr13 :103696347-103719196
Type of geneprotein-coding
RefGenesNM_000452.2,
Ensembl idENSG00000125255
DescriptionNa(+)-dependent ileal bile acid transporterileal apical sodium-dependent bile acid transporterileal sodium-dependent bile acid transporterileal sodium/bile acid cotransportersodium/taurocholate cotransporting polypeptide, ilealsolute carrier family 1
Modification date20141207
dbXrefs MIM : 601295
HGNC : HGNC
Ensembl : ENSG00000125255
HPRD : 03189
Vega : OTTHUMG00000017313
ProteinUniProt: Q12908
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC10A2
BioGPS: 6555
Gene Expression Atlas: ENSG00000125255
The Human Protein Atlas: ENSG00000125255
PathwayNCI Pathway Interaction Database: SLC10A2
KEGG: SLC10A2
REACTOME: SLC10A2
ConsensusPathDB
Pathway Commons: SLC10A2
MetabolismMetaCyc: SLC10A2
HUMANCyc: SLC10A2
RegulationEnsembl's Regulation: ENSG00000125255
miRBase: chr13 :103,696,347-103,719,196
TargetScan: NM_000452
cisRED: ENSG00000125255
ContextiHOP: SLC10A2
cancer metabolism search in PubMed: SLC10A2
UCL Cancer Institute: SLC10A2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for SLC10A2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC10A2
Familial Cancer Database: SLC10A2
* 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_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 601295; gene.
613291; phenotype.
Orphanet
DiseaseKEGG Disease: SLC10A2
MedGen: SLC10A2 (Human Medical Genetics with Condition)
ClinVar: SLC10A2
PhenotypeMGI: SLC10A2 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC10A2

Mutations for SLC10A2
* 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 SLC10A2 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample             1   
GAIN (# sample)             1   
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=46)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr13:103698526-103698526p.S335L5
chr13:103698491-103698491p.E347K3
chr13:103704980-103704980p.I192T3
chr13:103701714-103701714p.E282Q2
chr13:103703730-103703730p.G213E2
chr13:103718278-103718278p.G108R2
chr13:103705025-103705025p.S177F2
chr13:103698508-103698508p.G341E2
chr13:103710711-103710711p.S133S2
chr13:103701654-103701654p.A302T2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample23 10  2    125112242 7
# mutation23 10  2    125112242 9
nonsynonymous SNV22 5  2    93  2171 4
synonymous SNV 1 5       3211 71 5
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
chr13:103698526p.S335L4
chr13:103703668p.G108R2
chr13:103698491p.T257M2
chr13:103718243p.E347K2
chr13:103698508p.G341E2
chr13:103718366p.L95I2
chr13:103718278p.P234S2
chr13:103701788p.I78I2
chr13:103718407p.P65S2
chr13:103718317p.V119V2

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 SLC10A2 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 SLC10A2

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

BLID,FAM228A,EGFEM1P,CARS2,F7,FAM101A,FAM150B,
FEZF1,FOLH1B,IMPG1,KRT86,LCN9,LOC157627,LOC285780,
OR2T11,OR6X1,PCID2,POU3F2,PTPRM,SLC10A2,TMEM27
ACE2,VSTM5,CACNA1B,CDK5R1,ESRRB,INPP5D,KRTAP4-12,
LCT,OR51F2,OR9A4,PIWIL4,PSORS1C2,SCARNA8,SLC10A2,
SNORA13,SPINK5,TBX10,TDO2,TGFA,TUBA4B,VSIG10L

C1orf61,CABS1,CCDC108,CCR9,CLCN1,CRISP1,EPHX3,
FAM131B,FAM99A,FAM99B,GOLGA6D,HS6ST3,NWD2,KRT76,
LOC415056,MT1B,OR2A12,OR4C15,SFRP5,SLC10A2,TRPM5
AADAC,APOA1,APOA4,APOB,APOC3,C17orf78,CCL25,
CPO,CRISP1,CUBN,DPEP1,FABP6,GSTA2,GSTA5,
KCNJ13,ONECUT3,SLC10A2,SL
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 SLC10A2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q12908; -.
ChemistryChEMBL CHEMBL2778; -.
ChemistryGuidetoPHARMACOLOGY 960; -.
Organism-specific databasesPharmGKB PA318; -.
Organism-specific databasesCTD 6555; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01248solute carrier family 10 (sodium/bile acid cotransporter family), member 2approved; investigationalDocetaxel
DB01041solute carrier family 10 (sodium/bile acid cotransporter family), member 2approved; withdrawn; investigationalThalidomide
DB00145solute carrier family 10 (sodium/bile acid cotransporter family), member 2approved; nutraceuticalGlycine


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Cross referenced IDs for SLC10A2
* 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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