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 AMPD2

Basic gene info.	Gene symbol	AMPD2
	Gene name	adenosine monophosphate deaminase 2
	Synonyms	PCH9\|SPG63
	Cytomap	UCSC genome browser: 1p13.3
	Genomic location	chr1 :110168048-110174677
	Type of gene	protein-coding
	RefGenes	NM_001257360.1, NM_001257361.1,NM_004037.7,NM_139156.3,NM_203404.1,
	Ensembl id	ENSG00000116337
	Description	AMP deaminase 2AMPDadenosine monophosphate deaminase 2 (isoform L)
	Modification date	20141207
dbXrefs	MIM : 102771
	HGNC : HGNC
	Ensembl : ENSG00000116337
	HPRD : 11808
	Vega : OTTHUMG00000011649
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AMPD2
	BioGPS: 271
	Gene Expression Atlas: ENSG00000116337
	The Human Protein Atlas: ENSG00000116337
Pathway	NCI Pathway Interaction Database: AMPD2
	KEGG: AMPD2
	REACTOME: AMPD2
	ConsensusPathDB
	Pathway Commons: AMPD2
Metabolism	MetaCyc: AMPD2
	HUMANCyc: AMPD2
Regulation	Ensembl's Regulation: ENSG00000116337
	miRBase: chr1 :110,168,048-110,174,677
	TargetScan: NM_001257360
	cisRED: ENSG00000116337
Context	iHOP: AMPD2
	cancer metabolism search in PubMed: AMPD2
	UCL Cancer Institute: AMPD2
Assigned class in ccmGDB	C

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Phenotypic Information for AMPD2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: AMPD2
	Familial Cancer Database: AMPD2

* 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_PURINE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: AMPD2
	MedGen: AMPD2 (Human Medical Genetics with Condition)
	ClinVar: AMPD2
Phenotype	MGI: AMPD2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: AMPD2

Mutations for AMPD2

* 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 AMPD2 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
BC030217	NEAT1	1	249	11	65190277	65190525	AMPD2	239	1691	1	110172058	110174677
BI021213	PCIF1	62	253	20	44566137	44566328	AMPD2	253	395	1	110174531	110174673

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=6)	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
chr1:110168351-110168351	p.S70N	1
chr1:110168805-110168805	p.R99Q	1
chr1:110168974-110168974	p.D125E	1
chr1:110169394-110169394	p.A166V	1
chr1:110170826-110170826	p.T374M	1
chr1:110170900-110170900	p.?	1
chr1:110173662-110173662	p.R762H	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=2

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		17	2		3		1			6	1	4	1	1	10	8	1	6
# mutation	2	1		18	2		3		1			6	1	4	1	1	10	9	1	7
nonsynonymous SNV	1	1		14	1		2		1			5	1	4	1	1	3	8	1	6
synonymous SNV	1			4	1		1					1					7	1		1

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
chr1:110173662	p.R724H,AMPD2	3
chr1:110172893	p.I609I,AMPD2	2
chr1:110170826	p.L8L,AMPD2	2
chr1:110168974	p.S303W,AMPD2	2
chr1:110172028	p.D87E,AMPD2	2
chr1:110168976	p.A528E,AMPD2	2
chr1:110163659	p.R88Q,AMPD2	2
chr1:110170727	p.T336K,AMPD2	2
chr1:110169934	p.R116C,AMPD2	1
chr1:110167965	p.Y135H,AMPD2	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 AMPD2 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 AMPD2

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


AMPD2,ARHGAP22,ATAD3A,ATXN7L2,CCDC102A,CTU2,E2F4, FHL3,KIFC3,MAP7D1,PLEKHM2,PLOD3,POLR2F,PPAN, PSRC1,RNF166,RRP1,SLC39A13,TMEM39B,WDR46,ZDHHC8	AMPD2,C17orf70,CACNB3,CNOT3,CXXC1,EHMT2,FBXL19, GPSM1,KRBA1,LLGL1,PITPNM1,POLD1,SEPT9,SLC12A9, SMO,SNAPC4,SRC,TCF3,TRAF7,TRIM28,TSC22D4

ALX3,AMIGO1,AMPD2,ATXN7L2,CYB561D1,DHX38,DPH2, DPH3P1,STRIP1,MROH1,INTS1,IPO13,JRK,MAFG, MCM3AP,NPHP4,PRDM15,SMG5,USP24,ZBTB40,ZCCHC14	AMPD2,ANAPC2,ANO8,C17orf70,CHPF,CPSF1,CUL9, DENND4B,LOC150197,MAN2A2,PCSK4,PDE4DIP,POLM,PPP1R3E, SARM1,TCF3,TOP3B,TUBGCP6,WDR24,XPC,ZFP41

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 AMPD2

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
DB00173	adenosine monophosphate deaminase 2	approved; nutraceutical	Adenine
DB00640	adenosine monophosphate deaminase 2	approved; investigational	Adenosine

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Cross referenced IDs for AMPD2

* 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