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 AMY2B

Basic gene info.	Gene symbol	AMY2B
	Gene name	amylase, alpha 2B (pancreatic)
	Synonyms	AMY2\|AMY3\|HXA
	Cytomap	UCSC genome browser: 1p21
	Genomic location	chr1 :104097321-104122149
	Type of gene	protein-coding
	RefGenes	NM_020978.4,
	Ensembl id	ENSG00000240038
	Description	1,4-alpha-D-glucan glucanohydrolase 2Balpha-amylase 2Bcarcinoid alpha-amylaseglycogenase
	Modification date	20141207
dbXrefs	MIM : 104660
	HGNC : HGNC
	Ensembl : ENSG00000240038
	HPRD : 00095
	Vega : OTTHUMG00000011024
Protein	UniProt: P19961 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AMY2B
	BioGPS: 280
	Gene Expression Atlas: ENSG00000240038
	The Human Protein Atlas: ENSG00000240038
Pathway	NCI Pathway Interaction Database: AMY2B
	KEGG: AMY2B
	REACTOME: AMY2B
	ConsensusPathDB
	Pathway Commons: AMY2B
Metabolism	MetaCyc: AMY2B
	HUMANCyc: AMY2B
Regulation	Ensembl's Regulation: ENSG00000240038
	miRBase: chr1 :104,097,321-104,122,149
	TargetScan: NM_020978
	cisRED: ENSG00000240038
Context	iHOP: AMY2B
	cancer metabolism search in PubMed: AMY2B
	UCL Cancer Institute: AMY2B
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for AMY2B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: AMY2B
	Familial Cancer Database: AMY2B

* 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 UCEC ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_STARCH_AND_SUCROSE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	104660; gene.
Orphanet
Disease	KEGG Disease: AMY2B
	MedGen: AMY2B (Human Medical Genetics with Condition)
	ClinVar: AMY2B
Phenotype	MGI: AMY2B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: AMY2B

Mutations for AMY2B

* 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 AMY2B 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
AW583683	CADPS	1	117	3	62578345	62631434	AMY2B	110	247	1	104122016	104122153
BJ994441	PCK1	1	94	20	56136166	56136259	AMY2B	93	552	1	104108055	104114815
DB221809	SMEK2	2	137	2	55842586	55843732	AMY2B	133	499	1	104114175	104114879

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=63)	Stat. for Synonymous SNVs (# total SNVs=22)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=0)
	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
chr1:104114357-104114357	p.R45*	5
chr1:104117961-104117961	p.D332A	2
chr1:104122083-104122083	p.E499D	2
chr1:104116527-104116527	p.F237F	2
chr1:104116532-104116532	p.A239E	2
chr1:104115689-104115689	p.R107H	2
chr1:104116432-104116432	p.V206F	1
chr1:104118116-104118116	p.R352L	1
chr1:104122014-104122014	p.N476N	1
chr1:104114744-104114744	p.N61Y	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=3

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	2	3	1	3	2		6		4	1		10	7			1	10	11	2	13
# mutation	2	3	1	3	2		7		4	1		21	7			1	10	13	2	13
nonsynonymous SNV	1		1	3	2		6		4	1		16	6			1	9	12	2	9
synonymous SNV	1	3					1					5	1				1	1		4

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
chr1:104116527	p.R107H	2
chr1:104115689	p.R282S	2
chr1:104116981	p.F237F	2
chr1:104118116	p.R352L	2
chr1:104116508	p.A169S	1
chr1:104121941	p.D261D	1
chr1:104114826	p.S356N	1
chr1:104117906	p.A461S	1
chr1:104122083	p.G105G	1
chr1:104115802	p.Q171K	1

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 AMY2B 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 AMY2B

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


AMY2B,CACNG5,CBLN1,FEV,GAD2,INSRR,KCNH3, KRTAP27-1,LOC648740,MEP1B,NEUROD1,NRSN1,PIWIL1,RALYL, RNPC3,SAMD14,SNTG1,ST8SIA3,SYNGR4,TRPM3,WNT16	AHSA2,AMY2B,RUSC1-AS1,CCNL2,CELF6,CLK4,FAM13A-AS1, GOLGA6L10,LOC100131434,LOC221442,LOC648740,LY6G5B,MDM4,HNRNPU-AS1, PARP6,PPIEL,RNPC3,SEC31B,SLC25A27,ZMAT1,ZNF83

AMY2B,C6orf164,ECHDC2,FAM71F2,INE1,LENG8,LOC100131434, LOC221442,LOC648740,LOC91316,RNPC3,STRC,TAS2R5,TDRD6, TMEM178A,TRIM52,TTLL3,TUBGCP6,CFAP44,ZNF224,ZNF767P	AGAP4,AHSA2,AMY2B,BMS1P5,MROH7,CCDC39,CCNL2, CHKB-CPT1B,DNAH1,LINC01000,LOC100132247,LOC91316,RBM6,SEC31B, STX16,TBC1D3,TRIM66,TUBGCP6,UCKL1-AS1,VPS13A,ZC3H11A

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 AMY2B

There's no related Drug.

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Cross referenced IDs for AMY2B

* 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