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 AK1
Basic gene info.Gene symbolAK1
Gene nameadenylate kinase 1
SynonymsHTL-S-58j
CytomapUCSC genome browser: 9q34.1
Genomic locationchr9 :130628758-130640022
Type of geneprotein-coding
RefGenesNM_000476.2,
Ensembl idENSG00000106992
DescriptionAK 1ATP-AMP transphosphorylase 1ATP:AMP phosphotransferaseadenylate kinase isoenzyme 1adenylate monophosphate kinasemyokinasetestis secretory sperm binding protein Li 58j
Modification date20141207
dbXrefs MIM : 103000
HGNC : HGNC
Ensembl : ENSG00000106992
HPRD : 00046
Vega : OTTHUMG00000020722
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AK1
BioGPS: 203
Gene Expression Atlas: ENSG00000106992
The Human Protein Atlas: ENSG00000106992
PathwayNCI Pathway Interaction Database: AK1
KEGG: AK1
REACTOME: AK1
ConsensusPathDB
Pathway Commons: AK1
MetabolismMetaCyc: AK1
HUMANCyc: AK1
RegulationEnsembl's Regulation: ENSG00000106992
miRBase: chr9 :130,628,758-130,640,022
TargetScan: NM_000476
cisRED: ENSG00000106992
ContextiHOP: AK1
cancer metabolism search in PubMed: AK1
UCL Cancer Institute: AK1
Assigned class in ccmGDBC

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Phenotypic Information for AK1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AK1
Familial Cancer Database: AK1
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: AK1
MedGen: AK1 (Human Medical Genetics with Condition)
ClinVar: AK1
PhenotypeMGI: AK1 (International Mouse Phenotyping Consortium)
PhenomicDB: AK1

Mutations for AK1
* 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 AK1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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
There's no copy number variation information in COSMIC data for this gene.

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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=6)
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
chr9:130634196-130634196p.R77L2
chr9:130634103-130634103p.R108L2
chr9:130634130-130634130p.V99G1
chr9:130630320-130630320p.S184S1
chr9:130634138-130634138p.P96P1
chr9:130630328-130630328p.V182L1
chr9:130630633-130630633p.I161I1
chr9:130635071-130635071p.T35T1
chr9:130630638-130630638p.V160I1
chr9:130635089-130635089p.V29V1

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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
# sample1  1  1    2 2 1 1 3
# mutation1  1  1    2 2 1 1 3
nonsynonymous SNV   1  1      1   1 1
synonymous SNV1          2 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
chr9:130630320p.D119D1
chr9:130630328p.R108P1
chr9:130630633p.T35T1
chr9:130630642p.V29V1
chr9:130630646p.A192S1
chr9:130630695p.D191D1
chr9:130630759p.S184S1
chr9:130634103p.V182L1
chr9:130635071p.I161I1
chr9:130630298p.E158E1

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 AK1 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 AK1

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

AK1,BLOC1S1,LAMTOR4,SWI5,C9orf16,DPM2,DPP7,
EDF1,ENDOG,FIS1,FPGS,LOC440957,NTMT1,MPG,
NDUFA13,PHPT1,PTGES2,RNASEK,SSNA1,SURF2,TCEB2
ABLIM2,ADSSL1,AK1,ALDOA,BIN1,CKMT2,CLTCL1,
COX7A1,CUTC,FNDC5,HRC,KCNJ12,MYOM1,PDE4DIP,
PHKG1,PPAPDC3,PTP4A3,RRAD,SCN1B,SHISA4,TRIM7

AK1,ARF1,CIB1,COQ4,EDF1,F12,FPGS,
GUK1,JTB,MRPL17,MRPL24,MRPL55,MTX1,PMVK,
PSMD4,LAMTOR2,SEC61B,TOR2A,TPM3,TRIM11,ZNF511
AK1,AMTN,APOBEC3A,AQP8,PRR32,DUSP13,GAGE12J,
HDAC9,KRT34,KRTAP4-7,LCE1F,LCE4A,LOC25845,MAPRE3,
OR56B1,PROL1,SERPINB13,SERPINB4,SLC26A3,SLC9A3,SSX1,
SSX2,TMPRSS11A,TR
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 AK1
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
DB01717adenylate kinase 1experimentalBis(Adenosine)-5'-Pentaphosphate


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Cross referenced IDs for AK1
* 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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