Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	AMY1A
	Gene name	amylase, alpha 1A (salivary)
	Synonyms	AMY1
	Cytomap	UCSC genome browser: 1p21
	Genomic location	chr1 :104292278-104301311
	Type of gene	protein-coding
	RefGenes	NM_001008221.1, NM_004038.3,
	Ensembl id	ENSG00000237763
	Description	1,4-alpha-D-glucan glucanohydrolase 1alpha-amylase 1amylase, salivary, alpha-1Aglycogenasesalivary alpha-amylasesalivary amylase alpha 1A
	Modification date	20141207
dbXrefs	MIM : 104700
	HGNC : HGNC
	Ensembl : ENSG00000237763
	HPRD : 00096
	Vega : OTTHUMG00000011020
Protein	UniProt: P04745 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AMY1A
	BioGPS: 276
	Gene Expression Atlas: ENSG00000237763
	The Human Protein Atlas: ENSG00000237763
Pathway	NCI Pathway Interaction Database: AMY1A
	KEGG: AMY1A
	REACTOME: AMY1A
	ConsensusPathDB
	Pathway Commons: AMY1A
Metabolism	MetaCyc: AMY1A
	HUMANCyc: AMY1A
Regulation	Ensembl's Regulation: ENSG00000237763
	miRBase: chr1 :104,292,278-104,301,311
	TargetScan: NM_001008221
	cisRED: ENSG00000237763
Context	iHOP: AMY1A
	cancer metabolism search in PubMed: AMY1A
	UCL Cancer Institute: AMY1A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for AMY1A(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_STARCH_AND_SUCROSE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	104700; gene. 104701; gene. 104702; gene.
Orphanet
Disease	KEGG Disease: AMY1A
	MedGen: AMY1A (Human Medical Genetics with Condition)
	ClinVar: AMY1A
Phenotype	MGI: AMY1A (International Mouse Phenotyping Consortium)
Phenotype	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.

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 AMY1A related fusion information.

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

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=1

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Somatic 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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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
chr1:104198984-104198984	p.G11A	1
chr1:104202090-104202090	p.V268G	1
chr1:104203067-104203067	p.A322T	1
chr1:104203082-104203082	p.I327V	1
chr1:104203222-104203222	p.F342Y	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# 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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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

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P04745; -.
Chemistry	ChEMBL	CHEMBL2478; -.
Organism-specific databases	PharmGKB	PA24783; -.
Organism-specific databases	CTD	276; -.
Organism-specific databases	CTD	277; -.
Organism-specific databases	CTD	278; -.

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
DB02379	amylase, alpha 1A (salivary)	experimental	Beta-D-Glucose
DB03088	amylase, alpha 1A (salivary)	experimental	Pyroglutamic Acid
DB03092	amylase, alpha 1A (salivary)	experimental	5-Hydroxymethyl-Chonduritol
DB03439	amylase, alpha 1A (salivary)	experimental	4,6-Dideoxy-4-Amino-Alpha-D-Glucose
DB04237	amylase, alpha 1A (salivary)	experimental	Tris(Hydroxyethyl)Aminomethane
DB00218	amylase, alpha 1A (salivary)	approved; investigational	Moxifloxacin

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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