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 AMY1A
Basic gene info.Gene symbolAMY1A
Gene nameamylase, alpha 1A (salivary)
SynonymsAMY1
CytomapUCSC genome browser: 1p21
Genomic locationchr1 :104292278-104301311
Type of geneprotein-coding
RefGenesNM_001008221.1,
NM_004038.3,
Ensembl idENSG00000237763
Description1,4-alpha-D-glucan glucanohydrolase 1alpha-amylase 1amylase, salivary, alpha-1Aglycogenasesalivary alpha-amylasesalivary amylase alpha 1A
Modification date20141207
dbXrefs MIM : 104700
HGNC : HGNC
Ensembl : ENSG00000237763
HPRD : 00096
Vega : OTTHUMG00000011020
ProteinUniProt: P04745
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AMY1A
BioGPS: 276
Gene Expression Atlas: ENSG00000237763
The Human Protein Atlas: ENSG00000237763
PathwayNCI Pathway Interaction Database: AMY1A
KEGG: AMY1A
REACTOME: AMY1A
ConsensusPathDB
Pathway Commons: AMY1A
MetabolismMetaCyc: AMY1A
HUMANCyc: AMY1A
RegulationEnsembl's Regulation: ENSG00000237763
miRBase: chr1 :104,292,278-104,301,311
TargetScan: NM_001008221
cisRED: ENSG00000237763
ContextiHOP: AMY1A
cancer metabolism search in PubMed: AMY1A
UCL Cancer Institute: AMY1A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for AMY1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AMY1A
Familial Cancer Database: AMY1A
* 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 104700; gene.
104701; gene.
104702; gene.
Orphanet
DiseaseKEGG Disease: AMY1A
MedGen: AMY1A (Human Medical Genetics with Condition)
ClinVar: AMY1A
PhenotypeMGI: AMY1A (International Mouse Phenotyping Consortium)
PhenomicDB: AMY1A

Mutations for AMY1A
* 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 AMY1A 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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=4)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
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
chr1:104202090-104202090p.V268G1
chr1:104203067-104203067p.A322T1
chr1:104203082-104203082p.I327V1
chr1:104203222-104203222p.F342Y1
chr1:104198984-104198984p.G11A1

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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=0

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                    
# mutation                    
nonsynonymous SNV                    
synonymous SNV                    
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

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 AMY1A 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 AMY1A

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

AMY1A,ZBED6CL,CASP5,CCL25,CD82,CHODL,CSAG3,
EPHB6,IDO1,IL15RA,LIPJ,LOC400759,MGC27382,ORM2,
PCP4L1,PGM1,PRSS55,RTP3,SFTPD,SLPI,TMEM38A
AMY1A,ARL4A,DSC3,HMGN4,ID4,KCNJ16,LPO,
MPPED2,MPZL2,MUC15,OLAH,OR52A5,PHYHIPL,SCD5,
SH3TC2,SLC17A2,SLC9A4,SSBP2,ST6GALNAC5,WFDC12,WFDC5

AMY1A,DUX4,ACTR3BP2,HSFX1,LCE2B,LOC728410,OR6N2,
OR8B3,PPIAL4B,PRAMEF17,PRAMEF3,RBMY1B,RPL13AP6,SNORA38,
SNORD104,SNORD16,SNORD35B,SNORD58C,SNORD62A,SNORD76,SNORD88B,
SNOR
AMY1A,AQP4,FAM181A-AS1,C4orf45,C7orf65,KRT17,LRP6,
MAGEA8,MYLK3,POU3F2,PSG5,RSF1,RSPH6A,SECISBP2L,
SENP6,SERPINB4,SKINTL,SPRR2D,TEX15,VSIG10L,ZIC5
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 AMY1A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P04745; -.
ChemistryChEMBL CHEMBL2478; -.
Organism-specific databasesPharmGKB PA24783; -.
Organism-specific databasesCTD 276; -.
Organism-specific databasesCTD 277; -.
Organism-specific databasesCTD 278; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02379amylase, alpha 1A (salivary)experimentalBeta-D-Glucose
DB03088amylase, alpha 1A (salivary)experimentalPyroglutamic Acid
DB03092amylase, alpha 1A (salivary)experimental5-Hydroxymethyl-Chonduritol
DB03439amylase, alpha 1A (salivary)experimental4,6-Dideoxy-4-Amino-Alpha-D-Glucose
DB04237amylase, alpha 1A (salivary)experimentalTris(Hydroxyethyl)Aminomethane
DB00218amylase, alpha 1A (salivary)approved; investigationalMoxifloxacin


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Cross referenced IDs for AMY1A
* 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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