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 CNDP2

Basic gene info.	Gene symbol	CNDP2
	Gene name	CNDP dipeptidase 2 (metallopeptidase M20 family)
	Synonyms	CN2\|CPGL\|HEL-S-13\|HsT2298\|PEPA
	Cytomap	UCSC genome browser: 18q22.3
	Genomic location	chr18 :72166822-72190689
	Type of gene	protein-coding
	RefGenes	NM_001168499.1, NM_018235.2,
	Ensembl id	ENSG00000133313
	Description	cytosolic non-specific dipeptidasecytosolic nonspecific dipeptidaseepididymis secretory protein Li 13glutamate carboxypeptidase-like protein 1peptidase A
	Modification date	20141222
dbXrefs	MIM : 169800
	HGNC : HGNC
	Ensembl : ENSG00000133313
	HPRD : 09893
	Vega : OTTHUMG00000132853
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CNDP2
	BioGPS: 55748
	Gene Expression Atlas: ENSG00000133313
	The Human Protein Atlas: ENSG00000133313
Pathway	NCI Pathway Interaction Database: CNDP2
	KEGG: CNDP2
	REACTOME: CNDP2
	ConsensusPathDB
	Pathway Commons: CNDP2
Metabolism	MetaCyc: CNDP2
	HUMANCyc: CNDP2
Regulation	Ensembl's Regulation: ENSG00000133313
	miRBase: chr18 :72,166,822-72,190,689
	TargetScan: NM_001168499
	cisRED: ENSG00000133313
Context	iHOP: CNDP2
	cancer metabolism search in PubMed: CNDP2
	UCL Cancer Institute: CNDP2
Assigned class in ccmGDB	C

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Phenotypic Information for CNDP2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CNDP2
	Familial Cancer Database: CNDP2

* 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_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: CNDP2
	MedGen: CNDP2 (Human Medical Genetics with Condition)
	ClinVar: CNDP2
Phenotype	MGI: CNDP2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CNDP2

Mutations for CNDP2

* 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
pancreas	CNDP2	chr18	72185587	72185607	CNDP2	chr18	72185671	72185691

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 CNDP2 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
BF853131	PAX8	11	248	2	114001208	114001444	CNDP2	237	497	18	72176191	72176450
AA367702	RYBP	1	211	3	72475567	72475777	CNDP2	211	404	18	72168680	72173247
BQ329957	CNDP2	2	255	18	72176197	72176450	PAX8	244	480	2	114001208	114001444
BI010777	CNDP2	12	261	18	72176191	72176440	FRYL	261	310	4	48741147	48741196
BI010769	CNDP2	21	255	18	72176204	72176440	PAX8	255	485	2	114001208	114001438
AI906669	CNDP2	10	184	18	72186290	72187366	ALKBH5	178	364	17	18112395	18112581
BF846333	CNDP2	28	269	18	72173231	72178184	CNDP2	266	443	18	72167146	72168618
BF814523	CNDP2	9	207	18	72163620	72167268	RPL9	200	407	4	39455744	39456258

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=46)	Stat. for Synonymous SNVs (# total SNVs=11)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr18:72168608-72168608	p.P35P	2
chr18:72183517-72183517	p.E320K	2
chr18:72183560-72183561	p.R334I	2
chr18:72178091-72178091	p.E167G	2
chr18:72185789-72185789	p.K375M	2
chr18:72173106-72173106	p.P76Q	2
chr18:72173110-72173110	p.L77L	2
chr18:72180851-72180851	p.A267V	1
chr18:72186318-72186318	p.E449K	1
chr18:72173170-72173170	p.Y97Y	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	2	1	12	2		3			1		5		2			9	5		4
# mutation	3	2	1	12	2		3			1		5		2			8	5		5
nonsynonymous SNV	2	2	1	9	2		1			1		2		2			2	4		2
synonymous SNV	1			3			2					3					6	1		3

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
chr18:72173110	p.K169K,CNDP2	2
chr18:72180810	p.L77L	2
chr18:72186318	p.G295G,CNDP2	1
chr18:72178113	p.Y97Y	1
chr18:72180828	p.G171G,CNDP2	1
chr18:72183552	p.V323A,CNDP2	1
chr18:72173106	p.H99R	1
chr18:72187269	p.I175I,CNDP2	1
chr18:72178114	p.L327F,CNDP2	1
chr18:72180833	p.S113S	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 CNDP2 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 CNDP2

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


ACSL5,ATP5A1,RBFA,TIMM21,C8orf34,CNDP2,CPT2, CTDP1,CYB5A,FECH,HADHA,LAP3,MRPL44,NARS, PPP2R4,TRAF7,TSPAN17,TXNL1,TXNL4A,UBE2L6,ZCCHC2	AP1M2,AP1S1,ATP13A1,ATP13A2,CNDP2,DAK,HYOU1, MAN1B1,MBOAT7,MTFP1,NANS,PDIA4,PRPF19,PVRL2, RANGAP1,RPS6KA1,RUVBL1,SMPD2,ST14,STXBP2,TMED3

ATP5A1,ATP9B,TIMM21,CDC42EP1,CNDP2,CXXC1,IRF1, KIAA1468,MBD2,MBP,ME2,MOCOS,MPDU1,NARS, PSMB10,SCO1,SOCS6,TNFSF13,TXNL4A,VPS4B,ZADH2	ACE2,ACY3,ANPEP,PLEKHS1,LINC00479,CA13,CDHR2, CNDP2,DGAT1,ESPL1,RMDN3,GK,GK3P,SLC52A1, HNF4G,MYO1A,PCK2,PLCB3,SLC2A5,SLC5A1,TM4SF20

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 CNDP2

There's no related Drug.

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Cross referenced IDs for CNDP2

* 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