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 GMDS
Basic gene info.Gene symbolGMDS
Gene nameGDP-mannose 4,6-dehydratase
SynonymsGMD|SDR3E1
CytomapUCSC genome browser: 6p25
Genomic locationchr6 :1624034-2245868
Type of geneprotein-coding
RefGenesNM_001253846.1,
NM_001500.3,
Ensembl idENSG00000112699
DescriptionGDP-D-mannose dehydrataseGDP-mannose 4,6 dehydrataseshort chain dehydrogenase/reductase family 3E, member 1
Modification date20141222
dbXrefs MIM : 602884
HGNC : HGNC
Ensembl : ENSG00000112699
HPRD : 11925
Vega : OTTHUMG00000016143
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GMDS
BioGPS: 2762
Gene Expression Atlas: ENSG00000112699
The Human Protein Atlas: ENSG00000112699
PathwayNCI Pathway Interaction Database: GMDS
KEGG: GMDS
REACTOME: GMDS
ConsensusPathDB
Pathway Commons: GMDS
MetabolismMetaCyc: GMDS
HUMANCyc: GMDS
RegulationEnsembl's Regulation: ENSG00000112699
miRBase: chr6 :1,624,034-2,245,868
TargetScan: NM_001253846
cisRED: ENSG00000112699
ContextiHOP: GMDS
cancer metabolism search in PubMed: GMDS
UCL Cancer Institute: GMDS
Assigned class in ccmGDBC

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Phenotypic Information for GMDS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GMDS
Familial Cancer Database: GMDS
* 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_FRUCTOSE_AND_MANNOSE_METABOLISM
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM

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

Mutations for GMDS
* 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
breastGMDSchr617200031720003FARS2chr657408965740896
breastGMDSchr621011532101553GMDSchr621189902119390
ovaryGMDSchr616415751641595GMDSchr616436021643622
ovaryGMDSchr616598341659854chr62251138722511407
ovaryGMDSchr616634891663509MPNDchr1943589074358927
ovaryGMDSchr616693461669366chr615948871594907
ovaryGMDSchr617030071703027GMDSchr616768341676854
ovaryGMDSchr617348711734891chr62277431922774339
ovaryGMDSchr617894221789442FDX1chr11110312497110312517
ovaryGMDSchr618345771834597chr612023641202384
ovaryGMDSchr619799261979946GMDSchr619682801968300
ovaryGMDSchr621403102140330chr93484049134840511
ovaryGMDSchr621646462164666chr54620065046200670
pancreasGMDSchr616332191633239GMDSchr617964991796519
pancreasGMDSchr616827911682811GMDSchr616830931683113
pancreasGMDSchr616827911682811GMDSchr616831031683123
pancreasGMDSchr616877571687777GMDSchr617375001737520
pancreasGMDSchr617064561706456GMDSchr618401071840107
pancreasGMDSchr617147991714819GMDSchr619205441920564
pancreasGMDSchr617586441758664GMDSchr618225451822565
pancreasGMDSchr617796331779653GMDSchr620494662049486
pancreasGMDSchr618313721831392LOC100508120chr623581682358188
pancreasGMDSchr618518061851826chr2434899873490007
pancreasGMDSchr619031411903161LOC100508120chr622915312291551
pancreasGMDSchr619523351952355GMDSchr618879341887954
pancreasGMDSchr620429872043007GMDSchr620435712043591
pancreasGMDSchr620737522073772chr62642047926420499
pancreasGMDSchr620795072079527GMDSchr620755162075536
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 GMDS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW375751TCP139976160201475160201533GMDS95262616985181698685
BG954532ERGIC161505172379197172379340GMDS141249621421632142271
BQ897638GMDS26132619051541905260PARVA126738111255090512551506
CV573848GMDS1114616264291626542GMDS110630616291921629712
BE002314GMDS23157618608501860984TLE115417698425345984253482
BE830483GMDS138160617927451792767ZNF843158290163144991831450050

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 # sample81 1  14 2 7  220  
GAIN (# sample)7  1  1 1 5  21  
LOSS (# sample)11    13 1 2   19  
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=31)		Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr6:2117747-2117747p.R64Q3
chr6:1961196-1961196p.S117F2
chr6:1961041-1961041p.E169K2
chr6:1742745-1742745p.E283K2
chr6:1726689-1726689p.H316H2
chr6:1742725-1742725p.F289L1
chr6:1961164-1961164p.D128Y1
chr6:2117775-2117775p.R55W1
chr6:1930370-1930370p.K246K1
chr6:1624425-1624425p.M366I1

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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
# sample23141 1 11 1011 17416
# mutation33141 1 11 1011 17418
nonsynonymous SNV3213  1 11 9    4215
synonymous SNV 1 11      111 132 3
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
chr6:1961196p.S87F,GMDS2
chr6:1742745p.R34Q,GMDS2
chr6:2117747p.R26L,GMDS2
chr6:2117771p.E253K,GMDS2
chr6:1726733p.G246W,GMDS1
chr6:2117772p.V118L,GMDS1
chr6:1930370p.M336I,GMDS1
chr6:1624425p.F241F,GMDS1
chr6:1961137p.D107Y,GMDS1
chr6:1742725p.E327K,GMDS1

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 GMDS 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 GMDS

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

C12orf45,ABRACL,RRP36,CALR,DDOST,DTNB,ENO1,
FOXC1,GMDS,HMBS,KIAA2013,LSM2,PLOD1,PSMC1,
PSMG4,SLC25A33,ST14,TIMM8B,TUBB,UQCRH,UQCRHL		AP1M2,DDOST,EPCAM,ERGIC3,F12,FXYD3,GINS2,
GMDS,H2AFY2,LAD1,MAGEF1,MARCKSL1,NIPSNAP1,NPM3,
OCIAD2,PIK3R2,PRPF19,RUVBL1,SMPDL3B,TMED3,TMEM125

AGR2,ANG,ASRGL1,ERN2,FCGBP,FHL2,FOXA3,
GMDS,GNPNAT1,HMG20B,L1TD1,LRRIQ4,MRAP2,NANS,
SERPINB1,SGSM3,SPDEF,ST6GALNAC1,TC2N,TFF3,XBP1		AK7,AURKA,COASY,COQ2,DARS2,DERL1,GALK2,
GMDS,HMGB3,HSD17B4,MIPEP,MMAA,MRAP2,NFE2L3,
NME2P1,PGD,RARS,RPN1,RTN4IP1,SRBD1,TPM3
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 GMDS
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02547GDP-mannose 4,6-dehydrataseexperimentalGuanosine-5'-Diphosphate-Rhamnose
DB04315GDP-mannose 4,6-dehydrataseexperimentalGuanosine-5'-Diphosphate


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Cross referenced IDs for GMDS
* 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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