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 SLC44A2
Basic gene info.Gene symbolSLC44A2
Gene namesolute carrier family 44 (choline transporter), member 2
SynonymsCTL2|PP1292
CytomapUCSC genome browser: 19p13.1
Genomic locationchr19 :10736170-10755235
Type of geneprotein-coding
RefGenesNM_001145056.1,
NM_020428.3,
Ensembl idENSG00000129353
Descriptioncholine transporter-like protein 2solute carrier family 44, member 2
Modification date20141207
dbXrefs MIM : 606106
HGNC : HGNC
Ensembl : ENSG00000129353
HPRD : 16198
Vega : OTTHUMG00000180585
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC44A2
BioGPS: 57153
Gene Expression Atlas: ENSG00000129353
The Human Protein Atlas: ENSG00000129353
PathwayNCI Pathway Interaction Database: SLC44A2
KEGG: SLC44A2
REACTOME: SLC44A2
ConsensusPathDB
Pathway Commons: SLC44A2
MetabolismMetaCyc: SLC44A2
HUMANCyc: SLC44A2
RegulationEnsembl's Regulation: ENSG00000129353
miRBase: chr19 :10,736,170-10,755,235
TargetScan: NM_001145056
cisRED: ENSG00000129353
ContextiHOP: SLC44A2
cancer metabolism search in PubMed: SLC44A2
UCL Cancer Institute: SLC44A2
Assigned class in ccmGDBC

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Phenotypic Information for SLC44A2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC44A2
Familial Cancer Database: SLC44A2
* 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: SLC44A2
MedGen: SLC44A2 (Human Medical Genetics with Condition)
ClinVar: SLC44A2
PhenotypeMGI: SLC44A2 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC44A2

Mutations for SLC44A2
* 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 SLC44A2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA801918NOP561532026372882637340SLC44A254450191071313110741815
BE765019SLC44A21484191075466710754737DST7127865632313956323346
BE068966SLC44A2182191074856410748738VCL75132107587853775878594
BF376932KCNIP122575170050712170050965SLC44A2250325191075408210754157
BF376933KCNIP112905170050678170050965SLC44A2283358191075408210754157

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   1      
GAIN (# sample)          1      
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=40)
Stat. for Synonymous SNVs
(# total SNVs=19)
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
chr19:10742214-10742214p.?3
chr19:10753110-10753110p.T666M2
chr19:10741819-10741819p.?2
chr19:10742609-10742609p.S231C2
chr19:10736975-10736975p.N28K2
chr19:10746124-10746124p.N389S2
chr19:10748698-10748698p.?2
chr19:10747068-10747068p.E435K2
chr19:10746180-10746180p.C408R2
chr19:10742770-10742770p.R254H2

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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
# sample121142 5 11 231  143111
# mutation121142 5 11 231  163112
nonsynonymous SNV11 91 2  1 221  9318
synonymous SNV 1151 3 1   1   7  4
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
chr19:10746124p.N387S,SLC44A22
chr19:10747040p.E204G,SLC44A21
chr19:10741976p.L331L,SLC44A21
chr19:10742750p.P480L,SLC44A21
chr19:10748382p.C35R,SLC44A21
chr19:10745669p.L218L,SLC44A21
chr19:10736971p.R337K,SLC44A21
chr19:10747042p.A495A,SLC44A21
chr19:10741983p.A41V,SLC44A21
chr19:10742769p.I234V,SLC44A21

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 SLC44A2 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 SLC44A2

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

ARHGEF9,NPR3,CARM1,CHST3,DNM2,DSG3,HRCT1,
KCNG1,KCNK5,KLF5,MFGE8,MICALL1,ROPN1B,SHC4,
SLC44A2,SMARCA4,SOX6,STK38,TMPRSS12,TRPV4,YIPF2
AP1M2,HID1,EMC10,CACFD1,CAPN1,CDK5,COMT,
DAK,GPR108,ITGA3,JUP,KRT7,LRSAM1,LSR,
MBOAT7,MPV17L2,PAFAH1B3,SCAMP4,SLC44A2,TMEM102,TSTD1

AHNAK,AKAP13,ASAP2,B4GALT1,CA12,IKZF2,LTBP4,
MMP28,PCDH1,PVRL4,RAPGEF3,RARG,ARHGEF28,RNASEL,
SGMS2,SLC44A2,TNKS1BP1,UNC5B,VSIG2,YIPF5,ZBTB7C
APOBR,ATP6AP1,CDH1,CLSTN1,CNNM2,EDC4,GAK,
GRAMD4,HNF4A,MARK2,MINK1,MVP,NR2F6,RAB19,
SCAP,SLC44A2,SLC9A1,SREBF2,TMEM63B,WWP2,ZBTB7C
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 SLC44A2


There's no related Drug.
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Cross referenced IDs for SLC44A2
* 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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