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 SLC9A1
Basic gene info.Gene symbolSLC9A1
Gene namesolute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1
SynonymsAPNH|NHE-1|NHE1|PPP1R143
CytomapUCSC genome browser: 1p36.1-p35
Genomic locationchr1 :27425299-27481621
Type of geneprotein-coding
RefGenesNM_003047.4,
NR_046474.1,
Ensembl idENSG00000090020
DescriptionNa(+)/H(+) exchanger 1Na-Li countertransporterprotein phosphatase 1, regulatory subunit 143sodium/hydrogen exchanger 1solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)solute carrier family 9 (sod
Modification date20141207
dbXrefs MIM : 107310
HGNC : HGNC
Ensembl : ENSG00000090020
HPRD : 00123
Vega : OTTHUMG00000004271
ProteinUniProt: P19634
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC9A1
BioGPS: 6548
Gene Expression Atlas: ENSG00000090020
The Human Protein Atlas: ENSG00000090020
PathwayNCI Pathway Interaction Database: SLC9A1
KEGG: SLC9A1
REACTOME: SLC9A1
ConsensusPathDB
Pathway Commons: SLC9A1
MetabolismMetaCyc: SLC9A1
HUMANCyc: SLC9A1
RegulationEnsembl's Regulation: ENSG00000090020
miRBase: chr1 :27,425,299-27,481,621
TargetScan: NM_003047
cisRED: ENSG00000090020
ContextiHOP: SLC9A1
cancer metabolism search in PubMed: SLC9A1
UCL Cancer Institute: SLC9A1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for SLC9A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC9A1
Familial Cancer Database: SLC9A1
* 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_HYALURONAN_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 107310; gene.
Orphanet
DiseaseKEGG Disease: SLC9A1
MedGen: SLC9A1 (Human Medical Genetics with Condition)
ClinVar: SLC9A1
PhenotypeMGI: SLC9A1 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC9A1

Mutations for SLC9A1
* 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
pancreasSLC9A1chr12746221827462238MAP3K6chr12769321827693238
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 SLC9A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI992338SLC9A11212212742530727425417COL4A111831513110861195110862531
BQ369217PLOD3131217100853705100853900SLC9A110335912743429227436212
BQ369038PLOD3131217100853705100853900SLC9A110335912743429227436212
BF996876BCAT121260122496874924968990SLC9A125548212742921827432495

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 # sample1                
GAIN (# sample)                 
LOSS (# sample)1                
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=48)
Stat. for Synonymous SNVs
(# total SNVs=25)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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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
chr1:27427750-27427750p.T685M3
chr1:27440563-27440563p.I189M3
chr1:27440680-27440680p.G150G2
chr1:27429731-27429731p.E520K2
chr1:27429791-27429791p.R500W2
chr1:27440753-27440753p.S126*2
chr1:27428206-27428206p.?2
chr1:27436202-27436202p.G294S2
chr1:27426904-27426904p.A781V2
chr1:27427012-27427012p.S745I2

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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
# sample1328  1 11 332 1910 15
# mutation1328  1 11 332 1910 15
nonsynonymous SNV1116  1 1  13  147 7
synonymous SNV 212     1 2 2  53 8
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
chr1:27436074p.L336L2
chr1:27440680p.G294S2
chr1:27436202p.T685K2
chr1:27427750p.G150G2
chr1:27440563p.K560K1
chr1:27428548p.M115I1
chr1:27429181p.D758D1
chr1:27480641p.K555N1
chr1:27436018p.I315I1
chr1:27426971p.F103F1

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 SLC9A1 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 SLC9A1

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

CASZ1,CDC42,DNAJC16,FAM174B,FARP2,KIAA1522,LDLRAP1,
MAN1C1,MKNK2,MUL1,PCDH1,RERE,RETSAT,SEPN1,
SLC44A4,SLC9A1,TMEM57,TRIM62,WDTC1,WFS1,ZNF385A
AP1M2,ARHGAP8,KDF1,CBLC,CRB3,DDR1,EFS,
EPHA1,IGSF9,ITGA3,KIAA1522,LMX1B,LRRC8E,LSR,
PAK4,PCNXL3,PROM2,SEZ6L2,SLC4A3,SLC9A1,SPINT1

BTNL8,STPG1,CAPN5,RHOV___CHP1,CLSTN1,DHDDS,HECTD3,
JOSD1,KIAA1522,LIMA1,LIPH,LRP10,MALL,MMP28,
PTPRH,SDCBP2,SHROOM3,SLC9A1,STYK1,TSPAN1,VILL
ARHGAP17,BTBD9,CDH1,CGN,CLSTN1,CNNM4,ELF4,
JUP,KIAA1671,KIF13B,MARK2,MGLL,MYH14,PCDH1,
RUNDC1,SLC9A1,TMEM127,TMEM164,TMEM63B,WIPF2,WWP2
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 SLC9A1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P19634; -.
ChemistryChEMBL CHEMBL2781; -.
Organism-specific databasesPharmGKB PA35928; -.
Organism-specific databasesCTD 6548; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00594solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1approvedAmiloride
DB02624solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1experimentalHomoserine Lactone


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Cross referenced IDs for SLC9A1
* 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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