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 AMT

Basic gene info.	Gene symbol	AMT
	Gene name	aminomethyltransferase
	Synonyms	GCE\|GCST\|GCVT\|NKH
	Cytomap	UCSC genome browser: 3p21.31
	Genomic location	chr3 :49454210-49460111
	Type of gene	protein-coding
	RefGenes	NM_000481.3, NM_001164710.1,NM_001164711.1,NM_001164712.1,NR_028435.1,
	Ensembl id	ENSG00000145020
	Description	aminomethyltransferase, mitochondrialglycine cleavage system T protein
	Modification date	20141219
dbXrefs	MIM : 238310
	HGNC : HGNC
	Ensembl : ENSG00000145020
	HPRD : 01997
	Vega : OTTHUMG00000156847
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AMT
	BioGPS: 275
	Gene Expression Atlas: ENSG00000145020
	The Human Protein Atlas: ENSG00000145020
Pathway	NCI Pathway Interaction Database: AMT
	KEGG: AMT
	REACTOME: AMT
	ConsensusPathDB
	Pathway Commons: AMT
Metabolism	MetaCyc: AMT
	HUMANCyc: AMT
Regulation	Ensembl's Regulation: ENSG00000145020
	miRBase: chr3 :49,454,210-49,460,111
	TargetScan: NM_000481
	cisRED: ENSG00000145020
Context	iHOP: AMT
	cancer metabolism search in PubMed: AMT
	UCL Cancer Institute: AMT
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: AMT
	Familial Cancer Database: AMT

* 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_GLYCINE_SERINE_AND_THREONINE_METABOLISM KEGG_NITROGEN_METABOLISM

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

Mutations for AMT

* 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 AMT 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
AX747817	SMTN	2	2602	22	31497862	31500736	AMT	2599	2771	3	49454213	49454385
AK092939	SMTN	2	2602	22	31497862	31500736	AMT	2599	2771	3	49454213	49454385
DB332956	AMT	1	173	3	49454213	49454385	SMTN	170	557	22	31500349	31500736

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=13)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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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
chr3:49457688-49457688	p.V143L	2
chr3:49457734-49457734	p.L127L	2
chr3:49457752-49457752	p.N121N	2
chr3:49455139-49455139	p.S349N	2
chr3:49455277-49455277	p.I336N	1
chr3:49456807-49456807	p.G194G	1
chr3:49455006-49455006	p.P393P	1
chr3:49459597-49459597	p.T66T	1
chr3:49455330-49455330	p.R318R	1
chr3:49456843-49456843	p.?	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		3	1		1		1			1		1			1	4		3
# mutation	1	1		3	1		1		1			1		1			1	3		3
nonsynonymous SNV	1	1		1	1				1			1					1	2		2
synonymous SNV				2			1							1				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
chr3:49457752	p.N65N,AMT	2
chr3:49456775	p.P20L,AMT	1
chr3:49455006	p.P349P,AMT	1
chr3:49456802	p.R10H,AMT	1
chr3:49455073	p.R327H,AMT	1
chr3:49455114	p.K313N,AMT	1
chr3:49458983	p.L312L,AMT	1
chr3:49455119	p.S309F,AMT	1
chr3:49459684	p.E296K,AMT	1
chr3:49455127	p.I292N,AMT	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 AMT 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 AMT

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


AGER,AHSA2,AMT,APBB3,CCNL2,CHKB-CPT1B,FAM193B, LENG8,LOC338799,MST1P2,MYO15B,NEIL1,NSUN5P1,PILRB, SEC31B,CLASRP,SH2B1,SNRNP70,TTLL3,WASH7P,ZNF767P	AMT,ANKZF1,APBB3,CCNL2,CDK5RAP3,CENPT,FAM193B, HEMK1,HSF4,KAT2A,LPIN3,LUC7L,MST1,NEIL1, NSUN5P1,NSUN5P2,PILRB,PRSS50,SNRNP70,WASH7P,ZNF692

AMACR,AMT,ACTL10,CCDC113,ESPN,FUK,GFOD2, GRM8,LRRC2,NICN1,PAAF1,POLR3E,QPRT,RBM15B, RXFP4,SLC39A5,SMARCC1,SPIRE2,ZC3H18,ZNF345,ZNF662	ABHD14B,ADD3,AKR7A2,AMT,BTBD6,RRNAD1,CNFN, BLOC1S4,MNX1,P4HTM,PGAP2,PXMP2,RORC,SFT2D3, SLC35C2,SMPDL3B,TMEM191A,TMEM192,TMEM98,TYSND1,UGT2A3

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 AMT

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
DB00116	aminomethyltransferase	approved; nutraceutical	Tetrahydrofolic acid
DB00157	aminomethyltransferase	approved; nutraceutical	NADH
DB04789	aminomethyltransferase	experimental	5-methyltetrahydrofolate
DB00563	aminomethyltransferase	approved	Methotrexate

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Cross referenced IDs for AMT

* 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