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 SRR

Basic gene info.	Gene symbol	SRR
	Gene name	serine racemase
	Synonyms	ILV1\|ISO1
	Cytomap	UCSC genome browser: 17p13
	Genomic location	chr17 :2207247-2228553
	Type of gene	protein-coding
	RefGenes	NM_021947.1,
	Ensembl id	ENSG00000167720
	Description	D-serine ammonia-lyaseD-serine dehydrataseL-serine ammonia-lyaseL-serine dehydratase
	Modification date	20141207
dbXrefs	MIM : 606477
	HGNC : HGNC
	Ensembl : ENSG00000167720
	HPRD : 10451
	Vega : OTTHUMG00000090583
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SRR
	BioGPS: 63826
	Gene Expression Atlas: ENSG00000167720
	The Human Protein Atlas: ENSG00000167720
Pathway	NCI Pathway Interaction Database: SRR
	KEGG: SRR
	REACTOME: SRR
	ConsensusPathDB
	Pathway Commons: SRR
Metabolism	MetaCyc: SRR
	HUMANCyc: SRR
Regulation	Ensembl's Regulation: ENSG00000167720
	miRBase: chr17 :2,207,247-2,228,553
	TargetScan: NM_021947
	cisRED: ENSG00000167720
Context	iHOP: SRR
	cancer metabolism search in PubMed: SRR
	UCL Cancer Institute: SRR
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: SRR
	Familial Cancer Database: SRR

* 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

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

Mutations for SRR

* 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

* 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	SRR	chr17	2219606	2219626	SMG6	chr17	2130138	2130158
pancreas	SRR	chr17	2209364	2209384	SRR	chr17	2211109	2211129
pancreas	SRR	chr17	2214790	2214810		chr14	22043829	22043849

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 SRR 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
CN347172	SRR	1	541	17	2226860	2227400	ROMO1	539	601	20	34288835	34288897
AA614279	FUS	1	323	16	31202314	31202923	SRR	319	376	17	2208426	2208483

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=19)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr17:2221171-2221171	p.G59D	3
chr17:2218973-2218973	p.R40H	2
chr17:2227019-2227019	p.A292G	2
chr17:2224624-2224624	p.V142I	1
chr17:2227020-2227020	p.A292A	1
chr17:2221250-2221250	p.G85G	1
chr17:2224685-2224685	p.G162A	1
chr17:2227116-2227117	p.W325fs*5	1
chr17:2221269-2221269	p.T92P	1
chr17:2224836-2224836	p.V174F	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	3			3								1	1	1				4	1	4
# mutation	3			3								1	1	1				4	1	5
nonsynonymous SNV	2			3								1		1				4	1	4
synonymous SNV	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
chr17:2218973	p.R40H	2
chr17:2221250	p.A117G	1
chr17:2226491	p.Y127Y	1
chr17:2222127	p.P130S	1
chr17:2226566	p.V142I	1
chr17:2222158	p.P153P	1
chr17:2226989	p.G162A	1
chr17:2222174	p.G164R	1
chr17:2227145	p.V174F	1
chr17:2222205	p.Q219L	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 SRR 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 SRR

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


C17orf97,CYB5D1,CYB5D2,GLOD4,KIAA0753,LRRC48,MAP2K4, MED31,METTL16,PIGV,PNPLA4,RABEP1,RBKS,RNF167, SMG6,SRR,TMEM107,TTC19,YWHAE,ZBTB4,ZNF18	BLZF1,URI1,TRAPPC13,CPD,DHX29,ERGIC2,GOLGA5, ITFG1,JKAMP,MAP4K3,PIGB,PLA2G12A,RAB5A,RCN2, RNF141,RNF14,SCARB2,SRR,UBA5,UBE2K,UEVLD

ATPAF2,C17orf49,C17orf85,COPS3,DERL2,EIF4A1,GLOD4, MED11,MIS12,OVCA2,PEMT,RNF167,RNMTL1,RPA1, SLC25A11,SRR,STX8,TIMM22,TXNL1,UBE2G1,YWHAE	ARL3,FAM229B,CFAP36,COX7A1,CUEDC2,EIF5A2,FAM195B, KCNMB2,KIAA0895,MSANTD4,KPNA5,LAYN,NKIRAS1,NME4, NME5,SNRPN,SRR,TCEAL1,TCEAL7,TCEAL8,TMEM17

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 SRR

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	serine racemase	nutraceutical	Pyridoxal Phosphate
DB00133	serine racemase	approved; nutraceutical	L-Serine

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Cross referenced IDs for SRR

* 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