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 AHCYL2
Basic gene info.Gene symbolAHCYL2
Gene nameadenosylhomocysteinase-like 2
SynonymsADOHCYASE3
CytomapUCSC genome browser: 7q32.1
Genomic locationchr7 :128864854-129070052
Type of geneprotein-coding
RefGenesNM_001130720.2,
NM_001130722.2,NM_001130723.2,NM_015328.3,
Ensembl idENSG00000158467
DescriptionS-adenosyl-L-homocysteine hydrolase 3S-adenosylhomocysteine hydrolase-like 2putative adenosylhomocysteinase 3
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000158467
HPRD : 11113
Vega : OTTHUMG00000157677
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AHCYL2
BioGPS: 23382
Gene Expression Atlas: ENSG00000158467
The Human Protein Atlas: ENSG00000158467
PathwayNCI Pathway Interaction Database: AHCYL2
KEGG: AHCYL2
REACTOME: AHCYL2
ConsensusPathDB
Pathway Commons: AHCYL2
MetabolismMetaCyc: AHCYL2
HUMANCyc: AHCYL2
RegulationEnsembl's Regulation: ENSG00000158467
miRBase: chr7 :128,864,854-129,070,052
TargetScan: NM_001130720
cisRED: ENSG00000158467
ContextiHOP: AHCYL2
cancer metabolism search in PubMed: AHCYL2
UCL Cancer Institute: AHCYL2
Assigned class in ccmGDBC

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Phenotypic Information for AHCYL2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AHCYL2
Familial Cancer Database: AHCYL2
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: AHCYL2
MedGen: AHCYL2 (Human Medical Genetics with Condition)
ClinVar: AHCYL2
PhenotypeMGI: AHCYL2 (International Mouse Phenotyping Consortium)
PhenomicDB: AHCYL2

Mutations for AHCYL2
* 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
breastAHCYL2chr7128948688128949088COPG2chr7130313409130313809
ovaryAHCYL2chr7128954104128954124GUSBchr76543989265439912
prostateAHCYL2chr7128955544128955544NRF1chr7129381847129381847
prostateAHCYL2chr7128984258128984258chr7129401205129401205
prostateAHCYL2chr7128986933128986933chr7129407220129407220
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 AHCYL2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA731128AHCYL211127129050161129050272YME1L1111758102741247627425291
AK309708AHCYL211127129050161129050272YME1L11111064102740936727425291
AW793520AHCYL2663947128908993128909673PTGES3377437125706656357066765
AW947006CD244911121160810804160810825AHCYL21022457129069472129069615
DB138706CELF21292101120744711259477AHCYL22855707129062680129066320
BE070114AHCYL2993937128909372128909673PTGES3376436125706656357066765

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 # sample1  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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=47)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr7:129053510-129053510p.S481Y3
chr7:129019563-129019563p.Q150K2
chr7:129046260-129046260p.S416S2
chr7:128865054-128865054p.G46D2
chr7:128865055-128865055p.G46G2
chr7:129019506-129019506p.E131*2
chr7:129064755-129064755p.F534C2
chr7:129028979-129028979p.F186L2
chr7:129040167-129040167p.D287G2
chr7:129064971-129064971p.P566L2

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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
# sample211132 412  611  103 7
# mutation211132 412  611  93 7
nonsynonymous SNV21 112 412  411  73 6
synonymous SNV  12       2    2  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
chr7:129064755p.R490L,AHCYL22
chr7:129028979p.S170S,AHCYL22
chr7:129064971p.F533C,AHCYL22
chr7:129062691p.F185L,AHCYL22
chr7:129040167p.P565H,AHCYL22
chr7:129046260p.S415S,AHCYL22
chr7:129028934p.D286G,AHCYL22
chr7:128865045p.S148Y,AHCYL21
chr7:129049331p.G310A,AHCYL21
chr7:129028949p.Q149K,AHCYL21

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 AHCYL2 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 AHCYL2

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 AHCYL2


There's no related Drug.
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Cross referenced IDs for AHCYL2
* 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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