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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for AMY2A |
Basic gene info. | Gene symbol | AMY2A |
Gene name | amylase, alpha 2A (pancreatic) | |
Synonyms | AMY2|AMY2B|PA | |
Cytomap | UCSC genome browser: 1p21 | |
Genomic location | chr1 :104159998-104168400 | |
Type of gene | protein-coding | |
RefGenes | NM_000699.2, | |
Ensembl id | ENSG00000243480 | |
Description | 1,4-alpha-D-glucan glucanohydrolasealpha-amylaseamylase, pancreatic, alpha-2Afound in the pancreasglycogenasepancreatic alpha-amylasepancreatic amylase 2Apancreatic amylase alpha 2A | |
Modification date | 20141207 | |
dbXrefs | MIM : 104650 | |
HGNC : HGNC | ||
Ensembl : ENSG00000243480 | ||
HPRD : 00094 | ||
Vega : OTTHUMG00000011023 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_AMY2A | |
BioGPS: 279 | ||
Gene Expression Atlas: ENSG00000243480 | ||
The Human Protein Atlas: ENSG00000243480 | ||
Pathway | NCI Pathway Interaction Database: AMY2A | |
KEGG: AMY2A | ||
REACTOME: AMY2A | ||
ConsensusPathDB | ||
Pathway Commons: AMY2A | ||
Metabolism | MetaCyc: AMY2A | |
HUMANCyc: AMY2A | ||
Regulation | Ensembl's Regulation: ENSG00000243480 | |
miRBase: chr1 :104,159,998-104,168,400 | ||
TargetScan: NM_000699 | ||
cisRED: ENSG00000243480 | ||
Context | iHOP: AMY2A | |
cancer metabolism search in PubMed: AMY2A | ||
UCL Cancer Institute: AMY2A | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for AMY2A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: AMY2A |
Familial Cancer Database: AMY2A |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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_STARCH_AND_SUCROSE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: AMY2A |
MedGen: AMY2A (Human Medical Genetics with Condition) | |
ClinVar: AMY2A | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows AMY2A 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 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=33) | (# total SNVs=5) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr1:104166496-104166496 | p.N370N | 3 |
chr1:104160591-104160591 | p.E62* | 2 |
chr1:104160220-104160220 | p.G53E | 2 |
chr1:104166590-104166590 | p.R402* | 2 |
chr1:104160136-104160136 | p.R25P | 2 |
chr1:104160586-104160586 | p.P60L | 1 |
chr1:104162220-104162220 | p.E186D | 1 |
chr1:104160191-104160191 | p.C43C | 1 |
chr1:104163236-104163236 | p.E270* | 1 |
chr1:104162248-104162248 | p.E196K | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 | 1 | 1 | 1 | 3 |   |   | 2 |   |   |   |   | 4 |   | 1 |   |   | 5 | 3 | 1 | 6 |
# mutation | 1 | 1 | 1 | 3 |   |   | 2 |   |   |   |   | 6 |   | 1 |   |   | 5 | 3 | 1 | 6 |
nonsynonymous SNV | 1 | 1 | 1 | 3 |   |   | 2 |   |   |   |   | 6 |   | 1 |   |   | 4 | 3 | 1 | 4 |
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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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 |
chr1:104160673 | p.G89E | 2 |
chr1:104161613 | p.P59Q | 1 |
chr1:104160223 | p.V249G | 1 |
chr1:104162220 | p.E62K | 1 |
chr1:104160582 | p.E255E | 1 |
chr1:104162265 | p.P69H | 1 |
chr1:104160583 | p.G435V | 1 |
chr1:104162281 | p.E75K | 1 |
chr1:104160098 | p.P79A | 1 |
chr1:104160591 | p.V80F | 1 |
Other DBs for Point Mutations |
Copy 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 |
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. |
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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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for AMY2A |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
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 |
DB00284 | amylase, alpha 2A (pancreatic) | approved; investigational | Acarbose | ||
DB01922 | amylase, alpha 2A (pancreatic) | experimental | Maltosyl-Alpha (1,4)-D-Gluconhydroximo-1,5-Lactam | ||
DB02218 | amylase, alpha 2A (pancreatic) | experimental | N-[4-Hydroxymethyl-Cyclohexan-6-Yl-1,2,3-Triol]-4,6-Dideoxy-4-Aminoglucopyranoside | ||
DB02379 | amylase, alpha 2A (pancreatic) | experimental | Beta-D-Glucose | ||
DB02889 | amylase, alpha 2A (pancreatic) | experimental | 4-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 | ||
DB03088 | amylase, alpha 2A (pancreatic) | experimental | Pyroglutamic Acid | ||
DB03092 | amylase, alpha 2A (pancreatic) | experimental | 5-Hydroxymethyl-Chonduritol | ||
DB03439 | amylase, alpha 2A (pancreatic) | experimental | 4,6-Dideoxy-4-Amino-Alpha-D-Glucose | ||
DB03495 | amylase, alpha 2A (pancreatic) | experimental | 4,6-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 | ||
DB03773 | amylase, alpha 2A (pancreatic) | experimental | 6-Deoxy-Alpha-D-Glucose | ||
DB03971 | amylase, alpha 2A (pancreatic) | experimental | Acarbose Derived Hexasaccharide | ||
DB04453 | amylase, alpha 2A (pancreatic) | experimental | 4-O-(4,6-Dideoxy-4-{[4-[(4-O-Hexopyranosylhexopyranosyl)Oxy]-5,6-Dihydroxy-3-(Hydroxymethyl)Cyclohex-2-En-1-Yl]Amino}Hexopyranosyl)Hexopyranose | ||
DB04618 | amylase, alpha 2A (pancreatic) | experimental | 4,6-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 | ||
DB04465 | amylase, alpha 2A (pancreatic) | experimental | Lactose |
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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 |
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