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 ADSS

Basic gene info.	Gene symbol	ADSS
	Gene name	adenylosuccinate synthase
	Synonyms	ADEH\|ADSS 2
	Cytomap	UCSC genome browser: 1q44
	Genomic location	chr1 :244571793-244615436
	Type of gene	protein-coding
	RefGenes	NM_001126.3,
	Ensembl id	ENSG00000035687
	Description	AMPSase 2IMP--aspartate ligase 2L-type adenylosuccinate synthetaseadSS 2adenylosuccinate synthetase (Ade(-)H-complementing)adenylosuccinate synthetase isozyme 2adenylosuccinate synthetase, acidic isozymeadenylosuccinate synthetase, liver isozyme
	Modification date	20141207
dbXrefs	MIM : 103060
	HGNC : HGNC
	Ensembl : ENSG00000035687
	HPRD : 00050
	Vega : OTTHUMG00000040102
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ADSS
	BioGPS: 159
	Gene Expression Atlas: ENSG00000035687
	The Human Protein Atlas: ENSG00000035687
Pathway	NCI Pathway Interaction Database: ADSS
	KEGG: ADSS
	REACTOME: ADSS
	ConsensusPathDB
	Pathway Commons: ADSS
Metabolism	MetaCyc: ADSS
	HUMANCyc: ADSS
Regulation	Ensembl's Regulation: ENSG00000035687
	miRBase: chr1 :244,571,793-244,615,436
	TargetScan: NM_001126
	cisRED: ENSG00000035687
Context	iHOP: ADSS
	cancer metabolism search in PubMed: ADSS
	UCL Cancer Institute: ADSS
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: ADSS
	Familial Cancer Database: ADSS

* 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 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

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

Mutations for ADSS

* 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	ADSS	chr1	244595881	244596081	ADSS	chr1	244598415	244598615

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 ADSS related fusion information.

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

DB348377

ADSS

468

244572154

244572621

JMJD1C

465

537

64976007

64976078

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

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)

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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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=30)	Stat. for Synonymous SNVs (# total SNVs=17)

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
chr1:244587341-244587341	p.G165G	5
chr1:244574619-244574619	p.R430*	4
chr1:244587324-244587324	p.S171L	3
chr1:244579341-244579341	p.T370T	2
chr1:244582125-244582125	p.Y294Y	2
chr1:244580947-244580947	p.M351I	2
chr1:244583488-244583488	p.L258L	2
chr1:244582071-244582071	p.E312E	1
chr1:244601077-244601077	p.?	1
chr1:244583561-244583561	p.G234V	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=6

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			11			2					3	1	3			2	3	1	8
# mutation	2			8			2					3	1	3			2	4	1	8
nonsynonymous SNV	2			6			2					2	1	1			1	4		4
synonymous SNV				2								1		2			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
chr1:244587341	p.G165G	5
chr1:244583528	p.E312E	1
chr1:244600972	p.E108Q	1
chr1:244579368	p.Q288E	1
chr1:244586155	p.F94L	1
chr1:244614960	p.G278D	1
chr1:244579370	p.A54T	1
chr1:244587290	p.V276D	1
chr1:244614999	p.E41K	1
chr1:244580948	p.R430Q	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 ADSS 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 ADSS

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


ADSSL1,AK1,AKT1,BRF1,BTBD6,CCDC85C,CINP, CRIP2,GSTZ1,INF2,CEP170B,KLC1,MTA1,PACS2, PAK4,PWRN2,SIVA1,WBP1,WDR25,ZBTB42,ZFYVE21	ADSSL1,MLIP,C8orf22,CA3,CKMT2,CORO6,ENAM, FBXO40,HRC,KLHL33,MYH1,MYOM1,PDE4DIP,PGAM2, PYGM,SLC25A34,SLC25A4,SYPL2,TMEM52,TNNT3,TRIM7

ADSSL1,ALPPL2,BEX1,MRGPRG-AS1,LAMP5,C3orf35,FAM218A, CMAHP,CNTFR,FGF3,KCP,LOC100131551,MAEL,MAGED4, NTF4,OOSP2,SACS,SCN2A,SPANXN2,SUMO1P1,TM9SF1	AATK,ABCA4,ADSSL1,AGAP11,ALDH3B1,ALS2,AQP3, B3GALT2,MB21D2,MLXIPL,MPP6,PLLP,PNLIPRP2,RHBDL1, RNF141,SIRPA,SLC6A6,TEKT3,UNC93A,UPK3A,VNN1

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 ADSS

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
DB02109	adenylosuccinate synthase	experimental	Hadacidin
DB02493	adenylosuccinate synthase	experimental	Hydantocidin-5'-Phosphate
DB02666	adenylosuccinate synthase	experimental	(C8-R)-Hydantocidin 5'-Phosphate
DB02682	adenylosuccinate synthase	experimental	2-Deamino-6-Deoxy-6thiophosphite-5'-Phosphate Guanosine
DB02836	adenylosuccinate synthase	experimental	Guanosine 5'-Diphosphate 2':3'-Cyclic Monophosphate
DB02954	adenylosuccinate synthase	experimental	(Carboxyhydroxyamino)Ethanoic Acid
DB03146	adenylosuccinate synthase	experimental	2-Deazo-6-Thiophosphate Guanosine-5'-Monophosphate
DB04315	adenylosuccinate synthase	experimental	Guanosine-5'-Diphosphate
DB04460	adenylosuccinate synthase	experimental	(C8-S)-Hydantocidin 5'-Phosphate
DB04566	adenylosuccinate synthase	experimental	Inosinic Acid
DB04160	adenylosuccinate synthase	experimental	Diphosphate
DB00128	adenylosuccinate synthase	approved; nutraceutical	L-Aspartic Acid
DB03510	adenylosuccinate synthase	experimental	6-O-Phosphoryl Inosine Monophosphate
DB02580	adenylosuccinate synthase	experimental	1-(2-Methoxy-Ethoxy)-2-{2-[2-(2-Methoxy-Ethoxy]-Ethoxy}-Ethane
DB00864	adenylosuccinate synthase	approved; investigational	Tacrolimus

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Cross referenced IDs for ADSS

* 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