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 CSAD

Basic gene info.	Gene symbol	CSAD
	Gene name	cysteine sulfinic acid decarboxylase
	Synonyms	CSD\|PCAP
	Cytomap	UCSC genome browser: 12q13.11-q14.3
	Genomic location	chr12 :53551446-53574693
	Type of gene	protein-coding
	RefGenes	NM_001244705.1, NM_001244706.1,NM_015989.4,
	Ensembl id	ENSG00000139631
	Description	P-selectin cytoplasmic tail-associated proteincysteine sulfinic acid decarboxylase-related proteincysteine-sulfinate decarboxylasesulfinoalanine decarboxylase
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000139631
	HPRD : 16763
	Vega : OTTHUMG00000048076
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CSAD
	BioGPS: 51380
	Gene Expression Atlas: ENSG00000139631
	The Human Protein Atlas: ENSG00000139631
Pathway	NCI Pathway Interaction Database: CSAD
	KEGG: CSAD
	REACTOME: CSAD
	ConsensusPathDB
	Pathway Commons: CSAD
Metabolism	MetaCyc: CSAD
	HUMANCyc: CSAD
Regulation	Ensembl's Regulation: ENSG00000139631
	miRBase: chr12 :53,551,446-53,574,693
	TargetScan: NM_001244705
	cisRED: ENSG00000139631
Context	iHOP: CSAD
	cancer metabolism search in PubMed: CSAD
	UCL Cancer Institute: CSAD
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: CSAD
	Familial Cancer Database: CSAD

* 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_TAURINE_AND_HYPOTAURINE_METABOLISM REACTOME_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for CSAD

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

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 CSAD 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
BC053557	CSAD	1	2062	12	53574532	53582457	UQCRQ	2056	2110	5	132203325	132203379
AA805355	CSAD	1	159	12	53573481	53573639	CSAD	151	516	12	53569389	53569754
CK005588	CSAD	44	172	12	53551447	53551575	MEG3	158	633	14	101315053	101315530
BX093038	CXCL14	1	68	5	134907462	134907529	CSAD	57	437	12	53569583	53569963
AI032646	NFE2L2	1	366	2	178111745	178112110	CSAD	361	429	12	53552222	53552290
AA805343	CSAD	1	159	12	53573481	53573639	CSAD	151	495	12	53569389	53569733

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=27)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=1)	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
chr12:53552447-53552447	p.R444C	2
chr12:53564258-53564258	p.A199V	2
chr12:53553926-53553926	p.D382N	2
chr12:53553935-53553935	p.R379R	2
chr12:53554063-53554063	p.L336R	1
chr12:53566434-53566434	p.?	1
chr12:53564229-53564229	p.R209*	1
chr12:53552405-53552405	p.H458Y	1
chr12:53565756-53565756	p.A121T	1
chr12:53554090-53554090	p.R327H	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	2	1	1	5			2		1			3	2	2			3	10		5
# mutation	2	1	1	5			2		1			3	2	2			3	10		6
nonsynonymous SNV	1	1		4			2		1			3	1	2			3	8		6
synonymous SNV	1		1	1									1					2

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
chr12:53564258	p.R146R,CSAD	2
chr12:53553935	p.R94C,CSAD	2
chr12:53554091	p.A199V,CSAD	2
chr12:53564239	p.L135L,CSAD	1
chr12:53566220	p.G140G,CSAD	1
chr12:53553926	p.V123M,CSAD	1
chr12:53566323	p.V112M,CSAD	1
chr12:53564261	p.A121T,CSAD	1
chr12:53566324	p.D111N,CSAD	1
chr12:53553951	p.G104W,CSAD	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 CSAD 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 CSAD

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


AHSA2,APBB3,C19orf71,CCNL2,CSAD,D2HGDH,FAM193B, GIGYF1,GOLGA2P5,JMJD7-PLA2G4B,LENG8,LOC338799,MAPK8IP3,MYO15B, NEIL1,PILRB,RAPGEF3,RBM5,SRSF5,TTLL3,ZNF767P	AASS,ADCY6,FAM219B,ZNF436-AS1,CAPRIN2,CELF6,CSAD, DNAH1,DNHD1,FAM156A,FAM47E,GSDMB,INTS3,MAMDC4, NRBP2,PDP2,PHKA2,PLA2G6,PLCXD1,PRCD,TNPO2

AGAP4,AGAP6,AHSA2,APBB3,CCNL2,CHKB-CPT1B,CSAD, FAM193B,FNBP4,KIAA0895L,LENG8,LOC440944,LOC91316,LUC7L, LY6G5B,MAPK8IP3,NKTR,PILRB,TAF1C,TTLL3,WDR27	ADAMTS10,AGAP4,ANKRD23,CCDC57,CSAD,DNHD1,FAM156A, FAM193B,GIGYF1,GOLGA8A,HSF4,L3MBTL1,MEG3,NXF1, SIN3B,SLC25A27,STX16,TAF1C,TTLL3,WDR27,ZNF767P

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 CSAD

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
DB00114	cysteine sulfinic acid decarboxylase	nutraceutical	Pyridoxal Phosphate
DB00151	cysteine sulfinic acid decarboxylase	approved; nutraceutical	L-Cysteine

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Cross referenced IDs for CSAD

* 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