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 AGT

Basic gene info.	Gene symbol	AGT
	Gene name	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)
	Synonyms	ANHU\|SERPINA8
	Cytomap	UCSC genome browser: 1q42.2
	Genomic location	chr1 :230838271-230850336
	Type of gene	protein-coding
	RefGenes	NM_000029.3,
	Ensembl id	ENSG00000135744
	Description	alpha-1 antiproteinase, antitrypsinangiotensin Iangiotensin IIangiotensinogenpre-angiotensinogenserine (or cysteine) proteinase inhibitorserpin A8
	Modification date	20141222
dbXrefs	MIM : 106150
	HGNC : HGNC
	Ensembl : ENSG00000135744
	HPRD : 00106
	Vega : OTTHUMG00000037757
Protein	UniProt: P01019 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AGT
	BioGPS: 183
	Gene Expression Atlas: ENSG00000135744
	The Human Protein Atlas: ENSG00000135744
Pathway	NCI Pathway Interaction Database: AGT
	KEGG: AGT
	REACTOME: AGT
	ConsensusPathDB
	Pathway Commons: AGT
Metabolism	MetaCyc: AGT
	HUMANCyc: AGT
Regulation	Ensembl's Regulation: ENSG00000135744
	miRBase: chr1 :230,838,271-230,850,336
	TargetScan: NM_000029
	cisRED: ENSG00000135744
Context	iHOP: AGT
	cancer metabolism search in PubMed: AGT
	UCL Cancer Institute: AGT
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: AGT
	Familial Cancer Database: AGT

* 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
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	106150; gene. 145500; phenotype. 267430; phenotype.
Orphanet	243761; Essential hypertension. 97369; Renal tubular dysgenesis of genetic origin.
Disease	KEGG Disease: AGT
	MedGen: AGT (Human Medical Genetics with Condition)
	ClinVar: AGT
Phenotype	MGI: AGT (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: AGT

Mutations for AGT

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	AGT	chr1	230841684	230841704		chr1	230865748	230865768
ovary	AGT	chr1	230848219	230848239	AGT	chr1	230848329	230848349

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows AGT 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
DA142897	GABBR2	1	83	9	101051796	101051878	AGT	84	560	1	230846160	230849867
BP347159	AGT	1	536	1	230846101	230849867	GGCT	530	582	7	30544320	30544372

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=47)	Stat. for Synonymous SNVs (# total SNVs=23)

Stat. for Deletions (# total SNVs=3)	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
chr1:230846279-230846279	p.V106V	4
chr1:230846540-230846540	p.A19A	3
chr1:230845794-230845794	p.M268T	3
chr1:230838910-230838910	p.A479S	3
chr1:230846131-230846131	p.D156N	3
chr1:230846185-230846185	p.A138T	2
chr1:230841788-230841788	p.S339G	2
chr1:230840082-230840082	p.T376S	2
chr1:230846386-230846386	p.P71T	2
chr1:230846067-230846067	p.A177V	2

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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	2		9	1		4		1	3		7	4			3	9	5		15
# mutation	2	2		9	1		5		1	3		8	4			1	10	5		12
nonsynonymous SNV	1	2		6	1		2		1	3		5	1			1	7	3		8
synonymous SNV	1			3			3					3	3				3	2		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
chr1:230846067	p.A479S	3
chr1:230846279	p.V106V	3
chr1:230838910	p.A177E	3
chr1:230841942	p.K287N	2
chr1:230846235	p.R174R	1
chr1:230841702	p.A70S	1
chr1:230846414	p.N426S	1
chr1:230841909	p.S305N	1
chr1:230839063	p.F300L	1
chr1:230846251	p.S173P	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 AGT 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 AGT

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


A1CF,AGT,APCS,APOA2,APOA4,APOC3,ARG1, ASPDH,C8A,C8G,CRP,F2,FGF23,LEAP2, MT1B,PLG,PRAP1,SERPINA10,SERPINA7,SERPINC1,TM4SF5	ACAT1,ACO2,AGT,ALPK3,ATP5B,ADCK3,CHCHD3, FH,IMMT,MLYCD,OGDH,PDHB,PDHX,PGM1, PHYH,SDHB,SGCG,SLC2A4,SLC6A8,SOX6,TBX15

ABCC2,AGT,CLCN5,EMID1,F7,IL34,LRRC43, MYBPHL,NCKAP5,PHYHIPL,PKLR,PLAGL2,RASL10B,SALL1, SERPINA7,SHROOM4,SLC19A3,SLC23A1,SLC2A8,SLC5A6,TSPAN33	AGT,ASPDH,CLDN2,CRISP2,DSG3,RMDN3,GALNT14, GGN,GPD1,GRAMD1B,KCNJ16,KCP,MAF,NR1I3, PDZK1P1,PRSS1,SLC5A1,SLC7A7,TMEM92,UNC5CL,ZNF488

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 AGT

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA42; -.
Organism-specific databases	CTD	183; -.

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
DB00999	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Hydrochlorothiazide
DB00678	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Losartan
DB00790	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Perindopril
DB01197	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Captopril
DB00269	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Chlorotrianisene
DB00286	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Conjugated Estrogens
DB00890	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Dienestrol
DB00255	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Diethylstilbestrol
DB00783	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; investigational	Estradiol
DB00655	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Estrone
DB00977	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Ethinyl Estradiol
DB00394	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Beclomethasone
DB00443	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Betamethasone
DB01222	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; investigational	Budesonide
DB01410	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; investigational	Ciclesonide
DB01260	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; investigational	Desonide
DB01234	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; investigational	Dexamethasone
DB00180	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; investigational	Flunisolide
DB00588	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; investigational	Fluticasone Propionate
DB00741	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Hydrocortisone
DB00959	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Methylprednisolone
DB00764	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Mometasone
DB01384	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Paramethasone
DB00860	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Prednisolone
DB00635	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Prednisone
DB00896	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Rimexolone
DB00620	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Triamcinolone
DB00125	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; nutraceutical	L-Arginine
DB00155	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; nutraceutical	L-Citrulline
DB00435	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Nitric Oxide
DB00131	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; nutraceutical	Adenosine monophosphate
DB00171	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; nutraceutical	Adenosine triphosphate
DB00335	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Atenolol
DB00722	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; investigational	Lisinopril
DB01115	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved	Nifedipine
DB01258	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	approved; investigational	Aliskiren

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Cross referenced IDs for AGT

* 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