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 AK2
Basic gene info.Gene symbolAK2
Gene nameadenylate kinase 2
SynonymsADK2|AK 2
CytomapUCSC genome browser: 1p34
Genomic locationchr1 :33473540-33502512
Type of geneprotein-coding
RefGenesNM_001199199.1,
NM_001625.3,NM_013411.4,NR_037591.1,NR_037592.1,
Ensembl idENSG00000004455
DescriptionAK 2ATP-AMP transphosphorylase 2ATP:AMP phosphotransferaseadenylate kinase 2, mitochondrialadenylate kinase isoenzyme 2, mitochondrialadenylate monophosphate kinase
Modification date20141207
dbXrefs MIM : 103020
HGNC : HGNC
Ensembl : ENSG00000004455
HPRD : 00047
Vega : OTTHUMG00000004131
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AK2
BioGPS: 204
Gene Expression Atlas: ENSG00000004455
The Human Protein Atlas: ENSG00000004455
PathwayNCI Pathway Interaction Database: AK2
KEGG: AK2
REACTOME: AK2
ConsensusPathDB
Pathway Commons: AK2
MetabolismMetaCyc: AK2
HUMANCyc: AK2
RegulationEnsembl's Regulation: ENSG00000004455
miRBase: chr1 :33,473,540-33,502,512
TargetScan: NM_001199199
cisRED: ENSG00000004455
ContextiHOP: AK2
cancer metabolism search in PubMed: AK2
UCL Cancer Institute: AK2
Assigned class in ccmGDBC

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Phenotypic Information for AK2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AK2
Familial Cancer Database: AK2
* 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: AK2
MedGen: AK2 (Human Medical Genetics with Condition)
ClinVar: AK2
PhenotypeMGI: AK2 (International Mouse Phenotyping Consortium)
PhenomicDB: AK2

Mutations for AK2
* 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
ovaryAK2chr13348529733485317SURF4chr9136238594136238614
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 AK2 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1      
GAIN (# sample)          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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=11)
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
chr1:33502357-33502357p.G25R2
chr1:33502376-33502376p.A18A2
chr1:33480162-33480162p.H153H2
chr1:33502355-33502355p.G25G1
chr1:33487015-33487015p.I126I1
chr1:33487059-33487059p.D112N1
chr1:33487189-33487189p.?1
chr1:33478683-33478683p.S192*1
chr1:33487201-33487201p.A108E1
chr1:33478727-33478727p.?1

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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
# sample11 1  2 2  3 1  5  4
# mutation11 1  2 2  3 1  5  4
nonsynonymous SNV 1    1 1  3 1  3  2
synonymous SNV1  1  1 1       2  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
chr1:33480162p.H145H,AK22
chr1:33502361p.T186T,AK21
chr1:33480136p.P23P,AK21
chr1:33480173p.R178H,AK21
chr1:33478791p.R178C,AK21
chr1:33480187p.A174A,AK21
chr1:33478818p.R166C,AK21
chr1:33487015p.E162K,AK21
chr1:33478920p.P154R,AK21
chr1:33487201p.R142S,AK21

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 AK2 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 AK2

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

ADPRHL2,AK2,SMIM12,CDC20,EIF3I,ERI3,FAF1,
GNL2,HDGF,MAGOH,MED8,MRPL37,PSMB2,RCC1,
RRP1,TMEM39B,TRAPPC3,UQCRH,UQCRHL,YARS,ZBTB8OS
AK2,ATP5L,C14orf166,TMEM256,C20orf27,CMSS1,COX6A1,
COX7A2,HDDC2,LSM6,NDUFAF2,NIT2,PCBD1,PSMA6,
RPS20,SLC25A1,SNHG6,TBCA,THYN1,TMEM120A,TMEM14C

AK2,ATP5F1,ATPIF1,SMIM12,CHCHD1,EBNA1BP2,EIF2B3,
EIF3I,LAMTOR5,HDAC1,MRPL37,MRPS15,PSMA5,PSMB2,
RBBP4,SDHB,SNRNP40,UQCRH,UQCRHL,YARS,ZBTB8OS
AK2,ATP5C1,ATP5G3,C14orf142,C14orf2,C2orf47,ETFA,
GSTK1,HPRT1,MRPS28,MRPS36,MTCH2,NDUFA9,NDUFAB1,
PGK1,SAR1B,SDHB,EMC3,TMEM62,UQCRFS1,YWHAE
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 AK2


There's no related Drug.
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Cross referenced IDs for AK2
* 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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