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 ADK
Basic gene info.Gene symbolADK
Gene nameadenosine kinase
SynonymsAK
CytomapUCSC genome browser: 10q22|10q11-q24
Genomic locationchr10 :75910942-76469061
Type of geneprotein-coding
RefGenesNM_001123.3,
NM_001202449.1,NM_001202450.1,NM_006721.3,
Ensembl idENSG00000156110
Descriptionadenosine 5'-phosphotransferase
Modification date20141207
dbXrefs MIM : 102750
HGNC : HGNC
Ensembl : ENSG00000156110
HPRD : 00039
Vega : OTTHUMG00000018506
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ADK
BioGPS: 132
Gene Expression Atlas: ENSG00000156110
The Human Protein Atlas: ENSG00000156110
PathwayNCI Pathway Interaction Database: ADK
KEGG: ADK
REACTOME: ADK
ConsensusPathDB
Pathway Commons: ADK
MetabolismMetaCyc: ADK
HUMANCyc: ADK
RegulationEnsembl's Regulation: ENSG00000156110
miRBase: chr10 :75,910,942-76,469,061
TargetScan: NM_001123
cisRED: ENSG00000156110
ContextiHOP: ADK
cancer metabolism search in PubMed: ADK
UCL Cancer Institute: ADK
Assigned class in ccmGDBC

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Phenotypic Information for ADK(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ADK
Familial Cancer Database: ADK
* 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_PURINE_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

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

Mutations for ADK
* 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
breastADKchr107600316376003163chr108318308583183085
ovaryADKchr107599808175998101chr107719903577199055
ovaryADKchr107601139876011418ADKchr107601301576013035
ovaryADKchr107618701476187034ADKchr107618863876188658
ovaryADKchr107627855376278573ADKchr107641564776415667
ovaryADKchr107631724976317269chr193018101030181030
ovaryADKchr107639887776398897chr201972415319724173
ovaryADKchr107639889576398915chr201972903919729059
ovaryADKchr107644742576447445ADKchr107644240176442421
pancreasADKchr107622177076221790ADKchr107622171276221732
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 ADK related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE699173ADK1127107615399376158276LSAMP1282603115918507115918640
BM671160ADK53394107630047476300815ZNF64439042419139400791394181
AF092134RWDD1110726116894039116914431ADK10671087107596024175960261
BX098414TRIP1212792230702309230702588ADK268325107610121676101276

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 # sample14 16  2 1 3 123 1
GAIN (# sample)14  6  1   2   2  
LOSS (# sample)  1   1 1 1 122 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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=17)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr10:76429965-76429965p.V301A3
chr10:75960579-75960579p.D41E2
chr10:76468180-76468180p.P356S2
chr10:76349069-76349069p.G252G1
chr10:76468174-76468174p.T354P1
chr10:76153949-76153949p.G108G1
chr10:76360136-76360136p.?1
chr10:75960592-75960592p.D46N1
chr10:76153970-76153970p.I115I1
chr10:76360209-76360209p.V279M1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2 16  1  1      52 6
# mutation2 14  1  1      42 6
nonsynonymous SNV2 13  1  1      22 2
synonymous SNV   1            2  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
chr10:76429965p.V266A,ADK3
chr10:76468180p.P321S,ADK2
chr10:76074456p.G73G,ADK1
chr10:76349069p.I80I,ADK1
chr10:76074471p.I109I,ADK1
chr10:76360209p.K128T,ADK1
chr10:76074474p.E170K,ADK1
chr10:76360239p.A210V,ADK1
chr10:76153931p.R214T,ADK1
chr10:76429959p.G217G,ADK1

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 ADK 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 ADK

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

ADK,ANAPC16,ANXA7,AP3M1,ASCC1,CAMK2G,MICU1,
MCU,CHCHD1,DNAJC9,ECD,FAM149B1,LOC100128292,MRPS16,
P4HA1,PCBD1,PPA1,RPS24,SEC24C,VCL,VDAC2
ADK,AIG1,ALG14,DTD2,TMEM230,CYB5B,DCTN6,
FAM173B,FAM45A,HIGD1A,HNMT,ISCA1,LYRM1,METTL5,
MOCS2,RNF11,RNF14,STRAP,TMEM218,UBE2E2,VPS29

ADK,PARPBP,CMSS1,CCDC58,CMC1,DBI,DPY30,
ECD,HSPE1,MEMO1,MRPL48,MRPS16,MRPS23,NDUFAF2,
PNO1,SNRPG,TFAM,TRUB1,WDR12,YWHAQ,ZC3H15
ADK,BOLA3,CENPK,CKS1B,COQ3,DAP3,EXOSC8,
HSPE1,LSM3,LSM5,NHP2,NUP37,PPIA,PPIH,
RAN,RFC2,RFC4,SNRNP40,SNRPD1,SNRPE,SSBP1
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 ADK
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
DB00131adenosine kinaseapproved; nutraceuticalAdenosine monophosphate
DB00811adenosine kinaseapprovedRibavirin
DB07173adenosine kinaseexperimental7-(5-DEOXY-BETA-D-RIBOFURANOSYL)-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
DB07280adenosine kinaseexperimental5-[4-(DIMETHYLAMINO)PHENYL]-6-[(6-MORPHOLIN-4-YLPYRIDIN-3-YL)ETHYNYL]PYRIMIDIN-4-AMINE
DB00173adenosine kinaseapproved; nutraceuticalAdenine
DB00640adenosine kinaseapproved; investigationalAdenosine


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Cross referenced IDs for ADK
* 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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