Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	AHCY
	Gene name	adenosylhomocysteinase
	Synonyms	SAHH\|adoHcyase
	Cytomap	UCSC genome browser: 20q11.22
	Genomic location	chr20 :32868070-32899608
	Type of gene	protein-coding
	RefGenes	NM_000687.2, NM_001161766.1,
	Ensembl id	ENSG00000101444
	Description	S-adenosyl-L-homocysteine hydrolaseS-adenosylhomocysteine hydrolase
	Modification date	20141207
dbXrefs	MIM : 180960
	HGNC : HGNC
	Ensembl : ENSG00000101444
	HPRD : 01621
	Vega : OTTHUMG00000140098
Protein	UniProt: P23526 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AHCY
	BioGPS: 191
	Gene Expression Atlas: ENSG00000101444
	The Human Protein Atlas: ENSG00000101444
Pathway	NCI Pathway Interaction Database: AHCY
	KEGG: AHCY
	REACTOME: AHCY
	ConsensusPathDB
	Pathway Commons: AHCY
Metabolism	MetaCyc: AHCY
	HUMANCyc: AHCY
Regulation	Ensembl's Regulation: ENSG00000101444
	miRBase: chr20 :32,868,070-32,899,608
	TargetScan: NM_000687
	cisRED: ENSG00000101444
Context	iHOP: AHCY
	cancer metabolism search in PubMed: AHCY
	UCL Cancer Institute: AHCY
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of AHCY in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM KEGG_SELENOAMINO_ACID_METABOLISM REACTOME_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM	180960; gene. 613752; phenotype.
Orphanet	88618; Psychomotor retardation due to S-adenosylhomocysteine hydrolase deficiency.
Disease	KEGG Disease: AHCY
	MedGen: AHCY (Human Medical Genetics with Condition)
	ClinVar: AHCY
Phenotype	MGI: AHCY (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	AHCY	chr20	32884556	32884576	AHCY	chr20	32898751	32898771
pancreas	AHCY	chr20	32896721	32896741		chr20	39353648	39353668

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows AHCY related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
DB108079	LOC100507412	1	173	?	109618	109790	AHCY	173	580	20	32880286	32891161
BQ647045	AHCY	8	321	20	32878544	32879331	NPIPB7	316	805	16	28745873	28746783
DA207667	AHCY	1	104	20	32891060	32891163	SRRM2	99	559	16	2818917	2819377

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr20:32883218-32883218	p.V68I	3
chr20:32873405-32873405	p.I336I	2
chr20:32878157-32878157	p.K318M	2
chr20:32873245-32873245	p.?	2
chr20:32878605-32878605	p.R233Q	2
chr20:32880296-32880296	p.E105K	1
chr20:32878564-32878564	p.I247V	1
chr20:32883306-32883306	p.R38R	1
chr20:32868861-32868861	p.K426N	1
chr20:32879260-32879260	p.V175M	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		3		9			1					5	1				4	6		7
# mutation		3		9			1					5	1				4	8		7
nonsynonymous SNV		2		6			1					2	1				3	5		6
synonymous SNV		1		3								3					1	3		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr20:32883218	p.V68I,AHCY	2
chr20:32878616	p.L347L,AHCY	1
chr20:32873405	p.E155K,AHCY	1
chr20:32878689	p.E341K,AHCY	1
chr20:32883267	p.D122E,AHCY	1
chr20:32878141	p.I336I,AHCY	1
chr20:32878716	p.T117T,AHCY	1
chr20:32883282	p.P323P,AHCY	1
chr20:32878188	p.E108Q,AHCY	1
chr20:32879235	p.V308I,AHCY	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P23526; -.
Chemistry	ChEMBL	CHEMBL2664; -.
Chemistry	GuidetoPHARMACOLOGY	1233; -.
Organism-specific databases	PharmGKB	PA24636; -.
Organism-specific databases	CTD	191; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01907	adenosylhomocysteinase	experimental	Nicotinamide-Adenine-Dinucleotide
DB03216	adenosylhomocysteinase	experimental	(1'r,2's)-9-(2-Hydroxy-3'-Keto-Cyclopenten-1-Yl)Adenine
DB03273	adenosylhomocysteinase	experimental	3'-Oxo-Adenosine
DB03769	adenosylhomocysteinase	experimental	D-Eritadenine
DB07052	adenosylhomocysteinase	experimental	5'-S-ethyl-5'-thioadenosine
DB00640	adenosylhomocysteinase	approved; investigational	Adenosine
DB00134	adenosylhomocysteinase	approved; nutraceutical	L-Methionine
DB01033	adenosylhomocysteinase	approved	Mercaptopurine
DB00563	adenosylhomocysteinase	approved	Methotrexate

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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