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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 AASS

Basic gene info.	Gene symbol	AASS
	Gene name	aminoadipate-semialdehyde synthase
	Synonyms	LKR/SDH\|LKRSDH\|LORSDH
	Cytomap	UCSC genome browser: 7q31.3
	Genomic location	chr7 :121713597-121784344
	Type of gene	protein-coding
	RefGenes	NM_005763.3,
	Ensembl id	ENSG00000008311
	Description	alpha-aminoadipate semialdehyde synthasealpha-aminoadipic semialdehyde synthase, mitochondrialaminoadipic semialdehyde synthaselysine-2-oxoglutarate reductaselysine-ketoglutarate reductase /saccharopine dehydrogenase
	Modification date	20141207
dbXrefs	MIM : 605113
	HGNC : HGNC
	HPRD : 05489
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AASS
	BioGPS: 10157
	Gene Expression Atlas: ENSG00000008311
	The Human Protein Atlas: ENSG00000008311
Pathway	NCI Pathway Interaction Database: AASS
	KEGG: AASS
	REACTOME: AASS
	ConsensusPathDB
	Pathway Commons: AASS
Metabolism	MetaCyc: AASS
	HUMANCyc: AASS
Regulation	Ensembl's Regulation: ENSG00000008311
	miRBase: chr7 :121,713,597-121,784,344
	TargetScan: NM_005763
	cisRED: ENSG00000008311
Context	iHOP: AASS
	cancer metabolism search in PubMed: AASS
	UCL Cancer Institute: AASS
Assigned class in ccmGDB	C

Top

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

Cancer Description
Cancer	CGAP: AASS
	Familial Cancer Database: AASS

* 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_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for AASS

* 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

Top

- 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
pancreas	AASS	chr7	121721988	121722008	AASS	chr7	121725577	121725597
pancreas	AASS	chr7	121725032	121725052	AASS	chr7	121732575	121732595
pancreas	AASS	chr7	121742818	121742838	AASS	chr7	121732586	121732606

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 AASS 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
H48691	TLR8-AS1	12	122	X	12939334	12939444	AASS	116	423	7	121715791	121716095
H65666	TLR8-AS1	1	110	X	12939335	12939444	AASS	104	427	7	121715774	121716095
BX282586	TLR8-AS1	1	111	X	12939334	12939444	AASS	105	487	7	121715713	121716095

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

Top

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=5

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=109)	Stat. for Synonymous SNVs (# total SNVs=32)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

Top

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
chr7:121773699-121773699	p.V28I	3
chr7:121758477-121758477	p.S191C	3
chr7:121766507-121766507	p.R132C	3
chr7:121756793-121756793	p.T263M	3
chr7:121753238-121753238	p.P404P	2
chr7:121733186-121733186	p.L561P	2
chr7:121756972-121756972	p.V243L	2
chr7:121773726-121773726	p.G19S	2
chr7:121738539-121738539	p.L540L	2
chr7:121717989-121717989	p.T855T	2

Top

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	4	2		13	2		2		2			15	10	3			6	7		16
# mutation	4	2		13	2		2		2			16	12	3			6	8		17
nonsynonymous SNV	3	2		8	1				2			11	10	3			4	6		11
synonymous SNV	1			5	1		2					5	2				2	2		6

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])

Top

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
chr7:121758477	p.S191G	3
chr7:121756793	p.R132C	2
chr7:121766507	p.T263M	2
chr7:121738539	p.D69N	2
chr7:121773576	p.L540L	2
chr7:121718988	p.D805N	2
chr7:121766504	p.A325V	1
chr7:121741434	p.R143I	1
chr7:121773640	p.A35A	1
chr7:121719654	p.A747A	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 AASS 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]

Top

Gene Expression for AASS

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


AASS,ABCA10,C20orf194,CALCOCO1,CDC14B,CLCN6,CLK4, MICU3,GPRASP1,INTU,LAMA2,LCA5,LHFP,LOC286367, NPHP3,PLSCR4,RBM5,RHOJ,SPARCL1,TSHZ2,TTC28	AASS,AGPAT9,ALDH6A1,BCKDHB,C6,CALCRL,DNAH9, FAM161A,GMCL1,GYS2,LOC100190938,LPIN1,MAP3K5,MOGAT1, MPDZ,PLCXD1,PRKAG2,RNF125,RORB,ST3GAL6,STOX1

AASS,CBX7,CLSTN3,CRTC3,CRYBG3,CYP46A1,DYNC2H1, GLRB,ITPR1,KLF15,POU6F1,PRKCH,RFTN2,RHOQ, SEMA6C,TCEAL3,THSD1,TSPYL5,TTBK2,TTC28,USP51	AASS,ABLIM3,ADAM33,LINC00472,CHRD,COL16A1,COL27A1, COL5A2,GPR116,GPR133,GPR135,HIP1,MN1,MTR, PCDHGB3,PDZD2,PTPN13,REV3L,SASH1,STXBP1,TTC28

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for AASS

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
DB00142	aminoadipate-semialdehyde synthase	approved; nutraceutical	L-Glutamic Acid
DB00157	aminoadipate-semialdehyde synthase	approved; nutraceutical	NADH
DB02338	aminoadipate-semialdehyde synthase	experimental	Nadph Dihydro-Nicotinamide-Adenine-Dinucleotidephosphate
DB04207	aminoadipate-semialdehyde synthase	experimental	N-(5-Amino-5-Carboxypentyl)Glutamic Acid
DB00123	aminoadipate-semialdehyde synthase	approved; nutraceutical	L-Lysine

Top

Cross referenced IDs for AASS

* 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