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 AHCY
Basic gene info.Gene symbolAHCY
Gene nameadenosylhomocysteinase
SynonymsSAHH|adoHcyase
CytomapUCSC genome browser: 20q11.22
Genomic locationchr20 :32868070-32899608
Type of geneprotein-coding
RefGenesNM_000687.2,
NM_001161766.1,
Ensembl idENSG00000101444
DescriptionS-adenosyl-L-homocysteine hydrolaseS-adenosylhomocysteine hydrolase
Modification date20141207
dbXrefs MIM : 180960
HGNC : HGNC
Ensembl : ENSG00000101444
HPRD : 01621
Vega : OTTHUMG00000140098
ProteinUniProt: P23526
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AHCY
BioGPS: 191
Gene Expression Atlas: ENSG00000101444
The Human Protein Atlas: ENSG00000101444
PathwayNCI Pathway Interaction Database: AHCY
KEGG: AHCY
REACTOME: AHCY
ConsensusPathDB
Pathway Commons: AHCY
MetabolismMetaCyc: AHCY
HUMANCyc: AHCY
RegulationEnsembl's Regulation: ENSG00000101444
miRBase: chr20 :32,868,070-32,899,608
TargetScan: NM_000687
cisRED: ENSG00000101444
ContextiHOP: AHCY
cancer metabolism search in PubMed: AHCY
UCL Cancer Institute: AHCY
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of AHCY in cancer cell metabolism1. Loo LW, Tiirikainen M, Cheng I, Lum-Jones A, Seifried A, et al. (2013) Integrated analysis of genome-wide copy number alterations and gene expression in microsatellite stable, CpG island methylator phenotype-negative colon cancer. Genes Chromosomes Cancer 52: 450-466. doi: 10.1002/gcc.22043. pmid: 4019504. go to article

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Phenotypic Information for AHCY(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AHCY
Familial Cancer Database: AHCY
* 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_CYSTEINE_AND_METHIONINE_METABOLISM
KEGG_SELENOAMINO_ACID_METABOLISM
REACTOME_SULFUR_AMINO_ACID_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 180960; gene.
613752; phenotype.
Orphanet 88618; Psychomotor retardation due to S-adenosylhomocysteine hydrolase deficiency.
DiseaseKEGG Disease: AHCY
MedGen: AHCY (Human Medical Genetics with Condition)
ClinVar: AHCY
PhenotypeMGI: AHCY (International Mouse Phenotyping Consortium)
PhenomicDB: AHCY

Mutations for AHCY
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryAHCYchr203288455632884576AHCYchr203289875132898771
pancreasAHCYchr203289672132896741chr203935364839353668
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 AHCY related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB108079LOC1005074121173?109618109790AHCY173580203288028632891161
BQ647045AHCY8321203287854432879331NPIPB7316805162874587328746783
DA207667AHCY1104203289106032891163SRRM2995591628189172819377

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 1 1      
GAIN (# sample)      1 1 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=29)
Stat. for Synonymous SNVs
(# total SNVs=16)
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
chr20:32883218-32883218p.V68I3
chr20:32873405-32873405p.I336I2
chr20:32878157-32878157p.K318M2
chr20:32873245-32873245p.?2
chr20:32878605-32878605p.R233Q2
chr20:32880296-32880296p.E105K1
chr20:32878564-32878564p.I247V1
chr20:32883306-32883306p.R38R1
chr20:32868861-32868861p.K426N1
chr20:32879260-32879260p.V175M1

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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
# sample 3 9  1    51   46 7
# mutation 3 9  1    51   48 7
nonsynonymous SNV 2 6  1    21   35 6
synonymous SNV 1 3       3    13 1
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
chr20:32883218p.V68I,AHCY2
chr20:32878409p.C421Y,AHCY1
chr20:32880243p.A229A,AHCY1
chr20:32868877p.R36R,AHCY1
chr20:32883312p.H384Y,AHCY1
chr20:32878558p.R205L,AHCY1
chr20:32880258p.R36W,AHCY1
chr20:32873263p.E371K,AHCY1
chr20:32883314p.R196L,AHCY1
chr20:32878562p.P30L,AHCY1

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 AHCY 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 AHCY

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

AFF3,AHCYL2,BAZ2B,CHM,DMXL1,FAM73A,GCC2,
GLCE,HEATR5B,KIAA1324L,KLHDC10,MAP4K3,MED13L,MTMR10,
NAPEPLD,SLC25A40,THAP5,TMEM209,UBN2,WDR44,ZNF800
AHCYL2,CFAP126,CUL4A,CUL5,HBS1L,HECTD1,IPO7,
KIF1B,LOC729082,NEDD4,PPTC7,PRKAB2,PRKAR2A,PTCD3,
PYGO1,RNF115,UBR3,USO1,USP38,XPO4,ZYG11B

AHCYL2,AKR1B10,CA2,CEACAM7,CNNM4,CORO2A,DUOX2,
GPA33,IQGAP2,KRT20,LGR4,LIMA1,LIPH,MOB3B,
PLCE1,PLS1,PTPRH,RHBDL2,SLC2A13,SLC41A2,TSPAN1
ABHD3,AGFG2,AHCYL2,AMACR,CAPN2,CNNM4,DSG2,
MGLL,NCEH1,PDE6A,PDE8A,PIP5K1B,PPM1B,RAVER2,
SGK2,SH3BGRL2,SLC26A2,SLC26A3,SLC4A4,SNX30,TMEM65
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 AHCY
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P23526; -.
ChemistryChEMBL CHEMBL2664; -.
ChemistryGuidetoPHARMACOLOGY 1233; -.
Organism-specific databasesPharmGKB PA24636; -.
Organism-specific databasesCTD 191; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01907adenosylhomocysteinaseexperimentalNicotinamide-Adenine-Dinucleotide
DB03216adenosylhomocysteinaseexperimental(1'r,2's)-9-(2-Hydroxy-3'-Keto-Cyclopenten-1-Yl)Adenine
DB03273adenosylhomocysteinaseexperimental3'-Oxo-Adenosine
DB03769adenosylhomocysteinaseexperimentalD-Eritadenine
DB07052adenosylhomocysteinaseexperimental5'-S-ethyl-5'-thioadenosine
DB00640adenosylhomocysteinaseapproved; investigationalAdenosine
DB00134adenosylhomocysteinaseapproved; nutraceuticalL-Methionine
DB01033adenosylhomocysteinaseapprovedMercaptopurine
DB00563adenosylhomocysteinaseapprovedMethotrexate


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Cross referenced IDs for AHCY
* 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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