Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 SLC9A1

Basic gene info.	Gene symbol	SLC9A1
	Gene name	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1
	Synonyms	APNH\|NHE-1\|NHE1\|PPP1R143
	Cytomap	UCSC genome browser: 1p36.1-p35
	Genomic location	chr1 :27425299-27481621
	Type of gene	protein-coding
	RefGenes	NM_003047.4, NR_046474.1,
	Ensembl id	ENSG00000090020
	Description	Na(+)/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 date	20141207
dbXrefs	MIM : 107310
	HGNC : HGNC
	Ensembl : ENSG00000090020
	HPRD : 00123
	Vega : OTTHUMG00000004271
Protein	UniProt: P19634 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC9A1
	BioGPS: 6548
	Gene Expression Atlas: ENSG00000090020
	The Human Protein Atlas: ENSG00000090020
Pathway	NCI Pathway Interaction Database: SLC9A1
	KEGG: SLC9A1
	REACTOME: SLC9A1
	ConsensusPathDB
	Pathway Commons: SLC9A1
Metabolism	MetaCyc: SLC9A1
	HUMANCyc: SLC9A1
Regulation	Ensembl's Regulation: ENSG00000090020
	miRBase: chr1 :27,425,299-27,481,621
	TargetScan: NM_003047
	cisRED: ENSG00000090020
Context	iHOP: SLC9A1
	cancer metabolism search in PubMed: SLC9A1
	UCL Cancer Institute: SLC9A1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for SLC9A1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_HYALURONAN_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	107310; gene.
Orphanet
Disease	KEGG Disease: SLC9A1
	MedGen: SLC9A1 (Human Medical Genetics with Condition)
	ClinVar: SLC9A1
Phenotype	MGI: SLC9A1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	SLC9A1	chr1	27462218	27462238	MAP3K6	chr1	27693218	27693238

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SLC9A1 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AI992338	SLC9A1	12	122	1	27425307	27425417	COL4A1	118	315	13	110861195	110862531
BQ369217	PLOD3	13	121	7	100853705	100853900	SLC9A1	103	359	1	27434292	27436212
BQ369038	PLOD3	13	121	7	100853705	100853900	SLC9A1	103	359	1	27434292	27436212
BF996876	BCAT1	21	260	12	24968749	24968990	SLC9A1	255	482	1	27429218	27432495

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr1:27427750-27427750	p.T685M	3
chr1:27440563-27440563	p.I189M	3
chr1:27429791-27429791	p.R500W	2
chr1:27428206-27428206	p.?	2
chr1:27440753-27440753	p.S126*	2
chr1:27436202-27436202	p.G294S	2
chr1:27426904-27426904	p.A781V	2
chr1:27427012-27427012	p.S745I	2
chr1:27436074-27436074	p.L336L	2
chr1:27426905-27426905	p.A781T	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	3	2	8			1		1	1		3	3	2		1	9	10		15
# mutation	1	3	2	8			1		1	1		3	3	2		1	9	10		15
nonsynonymous SNV	1	1	1	6			1		1			1	3			1	4	7		7
synonymous SNV		2	1	2						1		2		2			5	3		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr1:27436074	p.G150G	2
chr1:27440680	p.L336L	2
chr1:27436202	p.G294S	2
chr1:27427750	p.T685K	2
chr1:27429731	p.S388N	1
chr1:27480681	p.I189L	1
chr1:27426972	p.R618C	1
chr1:27428600	p.L614L	1
chr1:27440593	p.S375F	1
chr1:27429791	p.L179L	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P19634; -.
Chemistry	ChEMBL	CHEMBL2781; -.
Organism-specific databases	PharmGKB	PA35928; -.
Organism-specific databases	CTD	6548; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00594	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	approved	Amiloride
DB02624	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	experimental	Homoserine 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