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 SLC44A5
Basic gene info.Gene symbolSLC44A5
Gene namesolute carrier family 44, member 5
SynonymsCTL5
CytomapUCSC genome browser: 1p31.1
Genomic locationchr1 :75667815-76076799
Type of geneprotein-coding
RefGenesNM_001130058.1,
NM_152697.4,
Ensembl idENSG00000137968
Descriptioncholine transporter-like protein 5
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000137968
HPRD : 14580
Vega : OTTHUMG00000009721
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC44A5
BioGPS: 204962
Gene Expression Atlas: ENSG00000137968
The Human Protein Atlas: ENSG00000137968
PathwayNCI Pathway Interaction Database: SLC44A5
KEGG: SLC44A5
REACTOME: SLC44A5
ConsensusPathDB
Pathway Commons: SLC44A5
MetabolismMetaCyc: SLC44A5
HUMANCyc: SLC44A5
RegulationEnsembl's Regulation: ENSG00000137968
miRBase: chr1 :75,667,815-76,076,799
TargetScan: NM_001130058
cisRED: ENSG00000137968
ContextiHOP: SLC44A5
cancer metabolism search in PubMed: SLC44A5
UCL Cancer Institute: SLC44A5
Assigned class in ccmGDBC

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Phenotypic Information for SLC44A5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC44A5
Familial Cancer Database: SLC44A5
* 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_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC44A5
MedGen: SLC44A5 (Human Medical Genetics with Condition)
ClinVar: SLC44A5
PhenotypeMGI: SLC44A5 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC44A5

Mutations for SLC44A5
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
haematopoietic_and_lymphoid_tissueSLC44A5chr17572960075729600chr17923931479239314
ovarySLC44A5chr17577263875772658PDZRN4chr124184771341847733
ovarySLC44A5chr17579433475794354SLC44A5chr17574622275746242
ovarySLC44A5chr17594192575941945SLC44A5chr17577449475774514
ovarySLC44A5chr17604913376049153chr136799156867991588
pancreasSLC44A5chr17572392775723947C1orf52chr18572176985721789
pancreasSLC44A5chr17577242475772624PDZRN4chr124184762741847827
pancreasSLC44A5chr17577263875772658PDZRN4chr124184771341847733
pancreasSLC44A5chr17580917175809191chr19752918897529208
pancreasSLC44A5chr17593082575930845SHBchr93798036837980388
skinSLC44A5chr17577983575779835chr1102967626102967626
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 SLC44A5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB455667SLC44A5210417600712076076745PLEKHA7102482111681135816812752
AW952701SLC44A57939917607180976072128ATP6V1C239545821092387610923956
AW772042ARL5A11432152659132152659274SLC44A512415917568625675686298
AI634522PARP1412803122449399122449678SLC44A526628517613544476135463
DA794004RABGGTB113217625193676253289SLC44A513360317568361975685577
AI702633PARP1412803122449399122449678SLC44A526628517613544476135463

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 # sample12  112 5 4  11 3
GAIN (# sample) 1  11  4 4  11 3
LOSS (# sample)11    2 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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=112)		Stat. for Synonymous SNVs
(# total SNVs=25)
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
chr1:75680342-75680342p.F584V5
chr1:75685015-75685015p.S398*4
chr1:75684294-75684294p.F470F4
chr1:75685020-75685020p.A396A4
chr1:75707705-75707705p.A171A4
chr1:75684184-75684184p.R507Q3
chr1:75685021-75685021p.A396V3
chr1:75684234-75684234p.M490I3
chr1:75704210-75704210p.G215E3
chr1:75681480-75681480p.E563K2

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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 213 6 4  2193  307 10
# mutation23 243 6 3  23103  337 11
nonsynonymous SNV22 203 3 3  1792  184 9
synonymous SNV 1 4  3    611  153 2
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
chr1:75707705p.A396A,SLC44A54
chr1:75685020p.A171A,SLC44A54
chr1:75684294p.V31F,SLC44A52
chr1:75679471p.K198N,SLC44A52
chr1:75672358p.F470F,SLC44A52
chr1:75805277p.F394F,SLC44A52
chr1:75708605p.F698F2
chr1:75704260p.L97L,SLC44A52
chr1:75716951p.R146H,SLC44A52
chr1:75685026p.L627L,SLC44A52

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 SLC44A5 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 SLC44A5

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

CA7,CADPS2,CHGB,CYBRD1,DCD,DLX2,ENTPD5,
EVX1,FGF14,LACRT,LIMCH1,NTN4,PIP,PPP3CA,
SEMA3E,SLC40A1,SLC44A5,SPATA6,ST8SIA6,TC2N,TRPV5		ALCAM,CROT,DOPEY2,ESRRG,FAM129A,G3BP2,HERC3,
LNX2,MBOAT2,MIOS,MSI2,NAA35,NUP62CL,PFKFB2,
PSME4,RAD1,SLC38A1,SLC44A5,SRP54,SYT6,TNIK

BDH2,CAMK2N1,CASC3,CEACAM18,CYB5B,DOK4,GNGT1,
GRAMD1C,MSL1,PPP1R1B,RAPGEFL1,RARA,SLC44A5,SNX32,
STXBP5L,TCAP,THRA,UBL3,UGT1A8,VPS36,WIPF2		ABHD12B,ABLIM2,BMP5,BSDC1,SWT1,C8orf33,DLL1,
EVX1,PTGDR2,GPRIN2,LOC149837,MCM9,MTM1,NEU2,
PANK1,SLC44A5,TFCP2L1,TMEM72,USP54,ZNF764,ZP1
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 SLC44A5


There's no related Drug.
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Cross referenced IDs for SLC44A5
* 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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