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 KDSR
Basic gene info.Gene symbolKDSR
Gene name3-ketodihydrosphingosine reductase
SynonymsDHSR|FVT1|SDR35C1
CytomapUCSC genome browser: 18q21.3
Genomic locationchr18 :60994970-61034506
Type of geneprotein-coding
RefGenesNM_002035.2,
Ensembl idENSG00000119537
Description3-dehydrosphinganine reductaseFVT-1KDS reductasefollicular lymphoma variant translocation 1follicular variant translocation protein 1short chain dehydrogenase/reductase family 35C, member 1
Modification date20141207
dbXrefs MIM : 136440
HGNC : HGNC
Ensembl : ENSG00000119537
HPRD : 00640
Vega : OTTHUMG00000132792
ProteinUniProt: Q06136
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KDSR
BioGPS: 2531
Gene Expression Atlas: ENSG00000119537
The Human Protein Atlas: ENSG00000119537
PathwayNCI Pathway Interaction Database: KDSR
KEGG: KDSR
REACTOME: KDSR
ConsensusPathDB
Pathway Commons: KDSR
MetabolismMetaCyc: KDSR
HUMANCyc: KDSR
RegulationEnsembl's Regulation: ENSG00000119537
miRBase: chr18 :60,994,970-61,034,506
TargetScan: NM_002035
cisRED: ENSG00000119537
ContextiHOP: KDSR
cancer metabolism search in PubMed: KDSR
UCL Cancer Institute: KDSR
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for KDSR(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: KDSR
Familial Cancer Database: KDSR
* 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
KEGG_SPHINGOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 136440; gene.
Orphanet
DiseaseKEGG Disease: KDSR
MedGen: KDSR (Human Medical Genetics with Condition)
ClinVar: KDSR
PhenotypeMGI: KDSR (International Mouse Phenotyping Consortium)
PhenomicDB: KDSR

Mutations for KDSR
* 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
pancreasKDSRchr186099817060998190C18orf34chr183082484930824869
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 KDSR related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA258694KDSR269186099600660996073CNN2683251910387841039041

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      2          
GAIN (# sample)                 
LOSS (# sample)      2          
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=10)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=1)
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
chr18:61022447-61022447p.S136T2
chr18:61022770-61022770p.V94V2
chr18:61030017-61030017p.N65H1
chr18:60999112-60999113p.R301fs*121
chr18:61018297-61018297p.N145Y1
chr18:61030020-61030021p.R64fs*21
chr18:60999113-60999113p.R301C1
chr18:61022445-61022445p.T137S1
chr18:61030059-61030059p.E51K1
chr18:61002517-61002517p.V284V1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   1  1    11   3214
# mutation   1  1    11   3215
nonsynonymous SNV   1       11   2213
synonymous SNV      1         1  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
chr18:60999113p.V284V1
chr18:61022741p.M273T1
chr18:61002517p.F263L1
chr18:61027014p.K231N1
chr18:61002551p.I168I1
chr18:61030017p.P152S1
chr18:61002580p.N145Y1
chr18:61011643p.T137S1
chr18:61018226p.L133I1
chr18:61018276p.N120I1

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 KDSR 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 KDSR

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

BCL2,C18orf25,HDHD2,IER3IP1,KDSR,TRAPPC8,KIAA1468,
LMAN1,MEX3C,NARS,PHLPP1,PIAS2,PIGN,PIK3C3,
RPRD1A,SMAD2,SMAD4,TMX3,VPS4B,ZNF24,ZNF271P
CASC4,CLDND1,CTSO,DPYD,EXOC1,FBXL3,HIAT1,
IDS,KDSR,LIN7C,LMBRD1,MIER1,NFE2L2,SEPT10,
SPTLC1,TM9SF3,TRAM1,TROVE2,TRPC1,TWSG1,YIPF5

ASPHD2,C18orf25,C18orf32,DAPK1,DUSP4,FECH,IER3IP1,
KDSR,MBP,MEX3C,NKX3-1,PMP22,RTTN,SLC39A6,
SMAD2,SMAD4,SOCS6,TMX3,TRIB2,VPS4B,ZCCHC2
ATP1B2,C1QTNF7,C7,CSDE1,CYP2U1,DDHD2,ECM2,
FAM172A,FLJ16779,GABARAPL1,GALNT16,KCND2,KDSR,LHFP,
NAP1L5,NR3C1,CPQ,RALYL,SVOP,SYN2,SYT4
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 KDSR


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