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 SLC44A1
Basic gene info.Gene symbolSLC44A1
Gene namesolute carrier family 44 (choline transporter), member 1
SynonymsCD92|CDW92|CHTL1|CTL1
CytomapUCSC genome browser: 9q31.2
Genomic locationchr9 :108006928-108153682
Type of geneprotein-coding
RefGenesNM_022109.2,
NM_001286730.1,NM_080546.4,
Ensembl idENSG00000070214
DescriptionCDW92 antigencholine transporter-like protein 1solute carrier family 44, member 1
Modification date20141207
dbXrefs MIM : 606105
HGNC : HGNC
Ensembl : ENSG00000070214
HPRD : 16197
Vega : OTTHUMG00000020421
ProteinUniProt: Q8WWI5
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC44A1
BioGPS: 23446
Gene Expression Atlas: ENSG00000070214
The Human Protein Atlas: ENSG00000070214
PathwayNCI Pathway Interaction Database: SLC44A1
KEGG: SLC44A1
REACTOME: SLC44A1
ConsensusPathDB
Pathway Commons: SLC44A1
MetabolismMetaCyc: SLC44A1
HUMANCyc: SLC44A1
RegulationEnsembl's Regulation: ENSG00000070214
miRBase: chr9 :108,006,928-108,153,682
TargetScan: NM_022109
cisRED: ENSG00000070214
ContextiHOP: SLC44A1
cancer metabolism search in PubMed: SLC44A1
UCL Cancer Institute: SLC44A1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for SLC44A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SLC44A1
Familial Cancer Database: SLC44A1
* 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 606105; gene.
Orphanet
DiseaseKEGG Disease: SLC44A1
MedGen: SLC44A1 (Human Medical Genetics with Condition)
ClinVar: SLC44A1
PhenotypeMGI: SLC44A1 (International Mouse Phenotyping Consortium)
PhenomicDB: SLC44A1

Mutations for SLC44A1
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasSLC44A1chr9108007269108007289RCAN2chr64645212946452149
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 SLC44A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CD050630NOTCH2222711120612011120612259SLC44A12644809108007210108007437
BX504871SLC44A111489108132314108132461KDM2A132233116702503167025132
C02459SLC44A111469108152447108152591SLC44A11403489108153184108153392

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     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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=51)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr9:108097968-108097968p.A132T4
chr9:108127819-108127819p.R437C3
chr9:108120671-108120671p.V239V2
chr9:108136923-108136923p.T513T2
chr9:108123483-108123483p.V258L2
chr9:108127850-108127850p.S447C2
chr9:108097969-108097969p.A132V2
chr9:108118629-108118629p.E213*2
chr9:108072074-108072074p.G66R1
chr9:108123571-108123571p.R287L1

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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
# sample 21141 2 1  712  76 8
# mutation 21141 2 1  912  77 8
nonsynonymous SNV 2 101 2 1  712  54 6
synonymous SNV  14       2    23 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
chr9:108127819p.A132V,SLC44A12
chr9:108127850p.R287L,SLC44A12
chr9:108127880p.T513T,SLC44A12
chr9:108097969p.R437C,SLC44A12
chr9:108136923p.S447C,SLC44A12
chr9:108123571p.R457Q,SLC44A12
chr9:108097866p.N285S,SLC44A11
chr9:108118546p.I459I,SLC44A11
chr9:108136967p.K145N,SLC44A11
chr9:108123589p.L489I,SLC44A11

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 SLC44A1 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 SLC44A1

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

ANO6,ARHGEF12,TMEM245,INIP,FAM120A,FAM120AOS,FAM172A,
FKTN,INPP4B,KIAA0430,MAP3K1,MARCH8,MEGF9,MFAP3,
RAB14,SLC44A1,SPIN1,SPTLC1,TSTD2,ZNF484,ZNF510
AFTPH,APH1B,CMTM6,DKFZP586I1420,ERBB4,ESR1,HHAT,
IQCH,LOC344595,MGAT4A,MYO6,JADE3,RAB6C,RERG,
SLC44A1,TMEM30B,TSPAN5,TSPYL4,TTC30B,UBP1,ZNRF2

FAM206A,C9orf85,CCDC28A,CD164,EPB41L4B,ERP44,FAM120AOS,
GALNT12,LRRC19,LRRC31,NIPSNAP3A,OSTF1,PDCL,PPP6C,
RAB14,SH3BGRL2,SLC35B3,SLC35D2,SLC44A1,SPTLC1,STX19
AHCYL2,ATP8B1,MCU,DSG2,ENTPD5,EPB41L4B,EPCAM,
FBXO34,GPR39,LGR4,PPARG,PPM1B,RASSF6,SH3BGRL2,
SLC35A3,SLC35B3,SLC44A1,TMEM170A,TMPRSS4,UGT8,XK
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 SLC44A1


There's no related Drug.
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Cross referenced IDs for SLC44A1
* 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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