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 AHCYL1
Basic gene info.Gene symbolAHCYL1
Gene nameadenosylhomocysteinase-like 1
SynonymsDCAL|IRBIT|PPP1R78|PRO0233|XPVKONA
CytomapUCSC genome browser: 1p13.2
Genomic locationchr1 :110527386-110566364
Type of geneprotein-coding
RefGenesNM_001242673.1,
NM_001242674.1,NM_001242675.1,NM_001242676.1,NM_006621.5,
Ensembl idENSG00000168710
DescriptionDC-expressed AHCY-like moleculeS-adenosyl homocysteine hydrolase homologS-adenosyl-L-homocysteine hydrolase 2S-adenosylhomocysteine hydrolase-like protein 1adoHcyase 2dendritic cell expressed AHCY-like proteininositol 1,4,5-trisphosphate receptor-bi
Modification date20141207
dbXrefs MIM : 607826
HGNC : HGNC
Ensembl : ENSG00000168710
HPRD : 07613
Vega : OTTHUMG00000011652
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AHCYL1
BioGPS: 10768
Gene Expression Atlas: ENSG00000168710
The Human Protein Atlas: ENSG00000168710
PathwayNCI Pathway Interaction Database: AHCYL1
KEGG: AHCYL1
REACTOME: AHCYL1
ConsensusPathDB
Pathway Commons: AHCYL1
MetabolismMetaCyc: AHCYL1
HUMANCyc: AHCYL1
RegulationEnsembl's Regulation: ENSG00000168710
miRBase: chr1 :110,527,386-110,566,364
TargetScan: NM_001242673
cisRED: ENSG00000168710
ContextiHOP: AHCYL1
cancer metabolism search in PubMed: AHCYL1
UCL Cancer Institute: AHCYL1
Assigned class in ccmGDBC

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Phenotypic Information for AHCYL1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AHCYL1
Familial Cancer Database: AHCYL1
* 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: AHCYL1
MedGen: AHCYL1 (Human Medical Genetics with Condition)
ClinVar: AHCYL1
PhenotypeMGI: AHCYL1 (International Mouse Phenotyping Consortium)
PhenomicDB: AHCYL1

Mutations for AHCYL1
* 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
breastAHCYL1chr1110543945110543945CAPZA1chr1113190387113190387
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 AHCYL1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CA841960MDC1188620051202005207AHCYL1825951110563832110564345
DA647181AHCYL115441110564420110564963LRRC585457823120047152120047390
AA207072AHCYL11241110535028110535051RNFT22114112117217168117217288
BQ774807AHCYL1181231110566259110566364AHCYL11207651110564873110565518
AI800578AHCYL111481110564858110565005AHCYL11435981110565532110565987
AI862468AHCYL112461110564750110564995CDK623747679236634192366578
BQ776309AHCYL11431110565797110566217AHCYL1286921110565596110566197
AA830163RBFOX214115223623427936234400AHCYL11054341110561072110563417
DA382933PDXDC11423161513037815130799AHCYL14156321110561585110562230

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      
GAIN (# sample)          1      
LOSS (# sample)        1        
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=38)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr1:110560608-110560608p.R365W3
chr1:110558115-110558115p.I248I2
chr1:110560120-110560120p.G323S2
chr1:110561083-110561083p.I404I2
chr1:110561085-110561085p.D405A2
chr1:110560622-110560622p.V369V2
chr1:110559066-110559066p.E295*2
chr1:110553838-110553838p.A79T2
chr1:110563436-110563436p.L517F2
chr1:110561051-110561051p.V394I1

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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
# sample1119  1 3 1623  18 6
# mutation1118  1 3 1623  18 7
nonsynonymous SNV 117  1 3  513   6 4
synonymous SNV1  1      111   12 3
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
chr1:110561083p.I357I,AHCYL12
chr1:110557445p.R167H,AHCYL12
chr1:110558117p.G273G,AHCYL11
chr1:110561048p.M441I,AHCYL11
chr1:110562203p.I75L,AHCYL11
chr1:110553923p.R318W,AHCYL11
chr1:110558120p.D454Y,AHCYL11
chr1:110561051p.A90T,AHCYL11
chr1:110562247p.R340H,AHCYL11
chr1:110553967p.A455V,AHCYL11

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 AHCYL1 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 AHCYL1

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

ABCD3,AHCYL1,ATP8B1,CPEB4,DBT,DNAJC16,DNAL1,
STRIP1,FAM73A,FBXL5,FPGT,GOLGB1,IPP,EFCAB14,
PCYOX1,SLC25A24,SPG11,STXBP3,TMEM167B,USP33,WDR47
AHCYL1,ASPH,ATP9A,CCPG1,COBLL1,DDHD2,DYNC1LI2,
IMPAD1,ITGB1,JAK1,KCTD20,KLHL5,PARVA,PCYOX1,
PTPN11,RABL3,RNF14,SEC22B,SEPT11,SNX19,STS

ABCD3,AGL,AHCYL1,ALG6,CEPT1,CLCC1,CSDE1,
DBT,DDAH1,FAM102B,GNAI3,HIPK1,MAGI3,PKN2,
RSBN1,SCP2,SERBP1,SLC25A24,SLC35A3,STXBP3,TAF13
AHCYL1,ALS2,AQP1,BCO2,CDR2L,CREB3L2,CYP2U1,
DEFB131,ESRRG,HOXC11,HOXC5,KCTD3,KIFC3,MAOB,
NBAS,PHYHIPL,PMP22,SFXN3,SUSD2,TIAM2,TMEM25
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 AHCYL1


There's no related Drug.
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Cross referenced IDs for AHCYL1
* 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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