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 CMPK1

Basic gene info.	Gene symbol	CMPK1
	Gene name	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic
	Synonyms	CK\|CMK\|CMPK\|UMK\|UMP-CMPK\|UMPK
	Cytomap	UCSC genome browser: 1p32
	Genomic location	chr1 :47799468-47844511
	Type of gene	protein-coding
	RefGenes	NM_001136140.1, NM_016308.2,NR_046394.1,NR_046395.1,
	Ensembl id	ENSG00000162368
	Description	CKUMP-CMP kinaseUMP/CMP kinasecytidylate kinasedCMP kinasedeoxycytidylate kinasenucleoside-diphosphate kinaseuridine monophosphate kinaseuridine monophosphate/cytidine monophosphate kinase
	Modification date	20141207
dbXrefs	MIM : 191710
	HGNC : HGNC
	Ensembl : ENSG00000162368
	HPRD : 18258
	Vega : OTTHUMG00000007849
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CMPK1
	BioGPS: 51727
	Gene Expression Atlas: ENSG00000162368
	The Human Protein Atlas: ENSG00000162368
Pathway	NCI Pathway Interaction Database: CMPK1
	KEGG: CMPK1
	REACTOME: CMPK1
	ConsensusPathDB
	Pathway Commons: CMPK1
Metabolism	MetaCyc: CMPK1
	HUMANCyc: CMPK1
Regulation	Ensembl's Regulation: ENSG00000162368
	miRBase: chr1 :47,799,468-47,844,511
	TargetScan: NM_001136140
	cisRED: ENSG00000162368
Context	iHOP: CMPK1
	cancer metabolism search in PubMed: CMPK1
	UCL Cancer Institute: CMPK1
Assigned class in ccmGDB	C

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Phenotypic Information for CMPK1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CMPK1
	Familial Cancer Database: CMPK1

* 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_PYRIMIDINE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES

Others
OMIM
Orphanet
Disease	KEGG Disease: CMPK1
	MedGen: CMPK1 (Human Medical Genetics with Condition)
	ClinVar: CMPK1
Phenotype	MGI: CMPK1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CMPK1

Mutations for CMPK1

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CMPK1 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
AA652040	CMPK1	1	124	1	47844277	47844400	CMPK1	121	230	1	47844398	47844507
BF873120	CMPK1	1	106	1	47820034	47820141	BANK1	88	115	4	102408760	102408789
BF891408	CMPK1	142	166	1	47827818	47827842	NOP58	154	349	2	203163103	203163500
AK027204	MRPS22	1	1128	3	139067310	139068439	CMPK1	1129	1937	1	47843702	47844507

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=11)	Stat. for Synonymous SNVs (# total SNVs=2)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr1:47834209-47834209	p.Q80H	2
chr1:47838719-47838719	p.N137K	1
chr1:47799639-47799639	p.G8R	1
chr1:47838725-47838725	p.T139T	1
chr1:47834152-47834152	p.Y61*	1
chr1:47838753-47838753	p.V149I	1
chr1:47834181-47834181	p.R71P	1
chr1:47840643-47840643	p.E178E	1
chr1:47840867-47840867	p.?	1
chr1:47834243-47834243	p.G92*	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=1

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					1	1	1				1		2
# mutation				2	1		1					1	1	1				1		2
nonsynonymous SNV				1			1					1	1	1						2
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
chr1:47840875	p.R71P	1
chr1:47834181	p.Y88Y	1
chr1:47842396	p.I99M	1
chr1:47834233	p.F72L,CMPK1	1
chr1:47834266	p.D75H,CMPK1	1
chr1:47838671	p.R79I,CMPK1	1
chr1:47838678	p.N88K,CMPK1	1
chr1:47838691	p.T90T,CMPK1	1
chr1:47838719	p.V100I,CMPK1	1
chr1:47838725	p.E129E,CMPK1	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 CMPK1 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 CMPK1

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


ATG4C,BTF3L4,CMPK1,DOCK7,FAF1,GPBP1L1,KCMF1, LRRC40,LRRC8B,NRD1,PPP1CB,PRPF38A,RLF,RNF11, SEP15,SERBP1,SH3GLB1,STIL,TMEM123,TXNDC12,ZNF644	CMPK1,CREBL2,ERI1,EXOC1,FAM200B,GMFB,GOLT1B, LMBRD1,LUZP6,MBNL2,NDFIP1,PLEKHA3,PPP2CB,PRKRIR, SLC35B3,SMAD2,TCEA1,TMEM167B,VAMP7,VPS26A,YIPF5

ABCD3,AKR1A1,C1orf210,C1orf50,TCEANC2,CMPK1,CPT2, FPGT,GJA9,GPBP1L1,MYCBP,OMA1,PIP5K1B,PPCS, RER1,RHBDL2,SCP2,SLC35A3,SUCLG2,TMEM59,ZMPSTE24	ARPC5,CALML4,CD164,CDC42SE2,CIB1,CMPK1,DAZAP2, GEMIN8P4,IL10RB,LRRC19,MYL12A,NDFIP2,RER1,SLC35A3, SLC35F5,SPTLC1,TMCO1,TMEM9B,TPMT,VAMP8,VTA1

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 CMPK1

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
DB00441	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic	approved	Gemcitabine
DB03403	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic	experimental	Cytidine-5'-Monophosphate
DB03431	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic	experimental	Adenosine-5'-Diphosphate
DB03435	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic	experimental	Uridine-5'-Diphosphate
DB03664	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic	experimental	P1-(Adenosine-5'-P5-(Uridine-5')Pentaphosphate
DB04444	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic	experimental	Tetrafluoroaluminate Ion
DB00987	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic	approved; investigational	Cytarabine
DB00709	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic	approved; investigational	Lamivudine
DB00544	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic	approved	Fluorouracil
DB00130	cytidine monophosphate (UMP-CMP) kinase 1, cytosolic	approved; nutraceutical; investigational	L-Glutamine

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Cross referenced IDs for CMPK1

* 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