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 AMY2A
Basic gene info.Gene symbolAMY2A
Gene nameamylase, alpha 2A (pancreatic)
SynonymsAMY2|AMY2B|PA
CytomapUCSC genome browser: 1p21
Genomic locationchr1 :104159998-104168400
Type of geneprotein-coding
RefGenesNM_000699.2,
Ensembl idENSG00000243480
Description1,4-alpha-D-glucan glucanohydrolasealpha-amylaseamylase, pancreatic, alpha-2Afound in the pancreasglycogenasepancreatic alpha-amylasepancreatic amylase 2Apancreatic amylase alpha 2A
Modification date20141207
dbXrefs MIM : 104650
HGNC : HGNC
Ensembl : ENSG00000243480
HPRD : 00094
Vega : OTTHUMG00000011023
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AMY2A
BioGPS: 279
Gene Expression Atlas: ENSG00000243480
The Human Protein Atlas: ENSG00000243480
PathwayNCI Pathway Interaction Database: AMY2A
KEGG: AMY2A
REACTOME: AMY2A
ConsensusPathDB
Pathway Commons: AMY2A
MetabolismMetaCyc: AMY2A
HUMANCyc: AMY2A
RegulationEnsembl's Regulation: ENSG00000243480
miRBase: chr1 :104,159,998-104,168,400
TargetScan: NM_000699
cisRED: ENSG00000243480
ContextiHOP: AMY2A
cancer metabolism search in PubMed: AMY2A
UCL Cancer Institute: AMY2A
Assigned class in ccmGDBC

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Phenotypic Information for AMY2A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AMY2A
Familial Cancer Database: AMY2A
* 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_STARCH_AND_SUCROSE_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: AMY2A
MedGen: AMY2A (Human Medical Genetics with Condition)
ClinVar: AMY2A
PhenotypeMGI: AMY2A (International Mouse Phenotyping Consortium)
PhenomicDB: AMY2A

Mutations for AMY2A
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows AMY2A 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
There's no copy number variation information in COSMIC data for this gene.

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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=33)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr1:104166496-104166496p.N370N3
chr1:104160220-104160220p.G53E2
chr1:104166590-104166590p.R402*2
chr1:104160136-104160136p.R25P2
chr1:104160591-104160591p.E62*2
chr1:104160098-104160098p.F12L1
chr1:104162281-104162281p.A207T1
chr1:104160213-104160213p.G51*1
chr1:104166536-104166536p.E384*1
chr1:104160642-104160642p.P79A1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1113  2    4 1  5316
# mutation1113  2    6 1  5316
nonsynonymous SNV1113  2    6 1  4314
synonymous SNV                1  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
chr1:104160673p.G89E2
chr1:104160098p.F12L1
chr1:104160591p.Q16L1
chr1:104162284p.D92N1
chr1:104160109p.P19Q1
chr1:104160613p.S132R1
chr1:104162293p.R25W1
chr1:104160118p.E186D1
chr1:104160630p.R25P1
chr1:104162316p.L201L1

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 AMY2A 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 AMY2A

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

ACTRT1,ADCYAP1,AMY2A,ATG9B,LINC00470___CHMP1B,TSPEAR,C6orf58,
CPLX1,DDX25,EPHA8,FSHB,INSM1,KRTAP12-1,LINC01512,
NHEG1,NMNAT2,PCSK1,PDZRN4,PRLHR,SIAH3,SLC35D3
AMY2A,AMY2B,TEX43,SAPCD1,CCDC84,CDK3,CRYGS,
CYP2D6,DFNB59,KLKB1,LMBR1L,LOC100272146,LOC284440,LUC7L,
LYG1,PRSS50,RETNLB,SLC23A3,TCP10,TMEM31,U2AF1L4

AMY2A,C11orf40,CELA2A,CELA2B,CELA3A,CELA3B,CLPS,
CPA1,CPB1,CTRB1,CTRB2,CTRC,CYP2W1,MAGIX,
OPRM1,PLA2G1B,PNLIP,PNLIPRP1,PSG8,SERPINI2,SYCN
AMY2A,ANKS6,C3orf62,CRTC2,CSAD,FAM156A,FAM193B,
FLJ34503,GHR,GOLGA8A,HERC2P2,KAAG1,KCTD19,KLHL17,
KSR2,LENG8,QRICH2,RGL3,STX16,TMEM80,TTLL3
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 AMY2A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00284amylase, alpha 2A (pancreatic)approved; investigationalAcarbose
DB01922amylase, alpha 2A (pancreatic)experimentalMaltosyl-Alpha (1,4)-D-Gluconhydroximo-1,5-Lactam
DB02218amylase, alpha 2A (pancreatic)experimentalN-[4-Hydroxymethyl-Cyclohexan-6-Yl-1,2,3-Triol]-4,6-Dideoxy-4-Aminoglucopyranoside
DB02379amylase, alpha 2A (pancreatic)experimentalBeta-D-Glucose
DB02889amylase, alpha 2A (pancreatic)experimental4-O-(4,6-Dideoxy-4-{[4,5,6-Trihydroxy-3-(Hydroxymethyl)Cyclohex-2-En-1-Yl]Amino}-Beta-D-Lyxo-Hexopyranosyl)-Alpha-D-Erythro-Hexopyranose
DB03088amylase, alpha 2A (pancreatic)experimentalPyroglutamic Acid
DB03092amylase, alpha 2A (pancreatic)experimental5-Hydroxymethyl-Chonduritol
DB03439amylase, alpha 2A (pancreatic)experimental4,6-Dideoxy-4-Amino-Alpha-D-Glucose
DB03495amylase, alpha 2A (pancreatic)experimental4,6-Dideoxy-4-{[4,5,6-Trihydroxy-3-(Hydroxymethyl)Cyclohex-2-En-1-Yl]Amino}-Alpha-D-Lyxo-Hexopyranosyl-(1->4)-Alpha-D-Threo-Hexopyranosyl-(1->6)-Alpha-L-Threo-Hexopyranose
DB03773amylase, alpha 2A (pancreatic)experimental6-Deoxy-Alpha-D-Glucose
DB03971amylase, alpha 2A (pancreatic)experimentalAcarbose Derived Hexasaccharide
DB04453amylase, alpha 2A (pancreatic)experimental4-O-(4,6-Dideoxy-4-{[4-[(4-O-Hexopyranosylhexopyranosyl)Oxy]-5,6-Dihydroxy-3-(Hydroxymethyl)Cyclohex-2-En-1-Yl]Amino}Hexopyranosyl)Hexopyranose
DB04618amylase, alpha 2A (pancreatic)experimental4,6-DIDEOXY-4-{[4-[(4-O-HEXOPYRANOSYLHEXOPYRANOSYL)OXY]-5,6-DIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}HEXOPYRANOSYL-(1->4)HEXOPYRANOSYL-(1->4)HEXOPYRANOSE
DB04465amylase, alpha 2A (pancreatic)experimentalLactose


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Cross referenced IDs for AMY2A
* 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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