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 PDXK

Basic gene info.	Gene symbol	PDXK
	Gene name	pyridoxal (pyridoxine, vitamin B6) kinase
	Synonyms	C21orf124\|C21orf97\|HEL-S-1a\|PKH\|PNK
	Cytomap	UCSC genome browser: 21q22.3
	Genomic location	chr21 :45138977-45182188
	Type of gene	protein-coding
	RefGenes	NM_003681.4, NM_021941.1,
	Ensembl id	ENSG00000160209
	Description	epididymis secretory sperm binding protein Li 1apyridoxal kinasepyridoxamine kinasepyridoxine kinasevitamin B6 kinase
	Modification date	20141207
dbXrefs	MIM : 179020
	HGNC : HGNC
	Ensembl : ENSG00000160209
	HPRD : 01526
	Vega : OTTHUMG00000086870
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PDXK
	BioGPS: 8566
	Gene Expression Atlas: ENSG00000160209
	The Human Protein Atlas: ENSG00000160209
Pathway	NCI Pathway Interaction Database: PDXK
	KEGG: PDXK
	REACTOME: PDXK
	ConsensusPathDB
	Pathway Commons: PDXK
Metabolism	MetaCyc: PDXK
	HUMANCyc: PDXK
Regulation	Ensembl's Regulation: ENSG00000160209
	miRBase: chr21 :45,138,977-45,182,188
	TargetScan: NM_003681
	cisRED: ENSG00000160209
Context	iHOP: PDXK
	cancer metabolism search in PubMed: PDXK
	UCL Cancer Institute: PDXK
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: PDXK
	Familial Cancer Database: PDXK

* 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_METABOLISM_OF_VITAMINS_AND_COFACTORS

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

Mutations for PDXK

* 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	PDXK	chr21	45144626	45144646	SLC26A9	chr1	205902519	205902539
pancreas	PDXK	chr21	45141428	45141448	LOC100506334	chr21	35329454	35329474

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 PDXK 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
L25496	C21orf2	25	247	21	45749348	45749570	PDXK	237	380	21	45157177	45157322
BF916410	PDXK	1	67	21	45179830	45179896	RAD9A	62	360	11	67165211	67165509
DA620160	LOC100507412	3	153	?	112029	112179	PDXK	151	256	21	45179047	45179152

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=7)	Stat. for Synonymous SNVs (# total SNVs=7)

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
chr21:45165994-45165994	p.G122G	2
chr21:45173479-45173479	p.S213F	2
chr21:45170384-45170384	p.L156L	1
chr21:45175603-45175603	p.T262A	1
chr21:45161591-45161591	p.L62L	1
chr21:45170387-45170387	p.L157L	1
chr21:45175615-45175615	p.V266I	1
chr21:45161602-45161602	p.Y66C	1
chr21:45170412-45170412	p.E166*	1
chr21:45175629-45175629	p.T270T	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			2									2	1			2	4		5
# mutation	2			2									2	1			2	4		4
nonsynonymous SNV				1										1				2		3
synonymous SNV	2			1									2				2	2		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
chr21:45165994	p.G122G	2
chr21:45173526	p.T85T	1
chr21:45163612	p.P286R	1
chr21:45173564	p.V111M	1
chr21:45163688	p.D121D	1
chr21:45173597	p.I147I	1
chr21:45165991	p.T148T	1
chr21:45175603	p.L156L	1
chr21:45175615	p.L157L	1
chr21:45168938	p.D181N	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 PDXK 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 PDXK

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


BTG3,FAM207A,CDC20,CDC42EP1,CEBPB,CSTB,ENO1, IRAK1,MICALL1,PDXK,PFKL,PFKP,PWP2,RRP1, RRP1B,SFT2D2,STK38,SUMO3,TTC7A,U2AF1,WDR4	AIFM2,BOK,CEBPA,CIDEC,DGAT1,ELMOD3,ESYT1, FAH,GPAM,GPD1,HEPACAM,HEPN1,LIPE,LPL, MARC1,NAT8L,NPR1,PDXK,PLEKHG6,PTH1R,RBP4

AGPAT3,C21orf33,FAM207A,C2CD2,MROH6,CSTB,DIP2A, CEP170B,LSS,MCM3AP,PCNT,PDXK,PFKL,PWP2, RPS6KA4,RRP1,RRP1B,SLC19A1,TMEM120B,U2AF1,UBE2G2	ABHD15,ACO2,AGPAT3,ARHGEF11,BAIAP2L2,EPN1,HECTD3, KIAA2013,KLF13,LAMB3,MGAT4B,MYO5B,MYO7B,NGEF, NHSL1,PDXK,PNPLA6,POR,PTK2B,SGK223,VIL1

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 PDXK

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
DB00147	pyridoxal (pyridoxine, vitamin B6) kinase	approved; nutraceutical	Pyridoxal
DB00165	pyridoxal (pyridoxine, vitamin B6) kinase	approved; nutraceutical	Pyridoxine
DB03431	pyridoxal (pyridoxine, vitamin B6) kinase	experimental	Adenosine-5'-Diphosphate
DB03909	pyridoxal (pyridoxine, vitamin B6) kinase	experimental	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate
DB04770	pyridoxal (pyridoxine, vitamin B6) kinase	experimental	O6-(R)-ROSCOVITINE, R-2-(6-BENZYLOXY-9-ISOPROPYL-9H-PURIN-2-YLAMINO)-BUTAN-1-OL
DB04776	pyridoxal (pyridoxine, vitamin B6) kinase	experimental	N6-METHYL-(R)-ROSCOVITINE, R-2-[6-(BENZYL-METHYL-AMINO)-9-ISOPROPYL-9H-PURIN-2-YLAMINO]-BUTAN-1-OL

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Cross referenced IDs for PDXK

* 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