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 PANK2

Basic gene info.	Gene symbol	PANK2
	Gene name	pantothenate kinase 2
	Synonyms	C20orf48\|HARP\|HSS\|NBIA1\|PKAN
	Cytomap	UCSC genome browser: 20p13
	Genomic location	chr20 :3869485-3904502
	Type of gene	protein-coding
	RefGenes	NM_024960.4, NM_153638.2,NM_153640.2,NM_153637.1,NM_153639.1, NM_153641.1,
	Ensembl id	ENSG00000125779
	Description	Hallervorden-Spatz syndromepantothenate kinase 2, mitochondrialpantothenic acid kinase 2
	Modification date	20141219
dbXrefs	MIM : 606157
	HGNC : HGNC
	Ensembl : ENSG00000125779
	Vega : OTTHUMG00000031768
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PANK2
	BioGPS: 80025
	Gene Expression Atlas: ENSG00000125779
	The Human Protein Atlas: ENSG00000125779
Pathway	NCI Pathway Interaction Database: PANK2
	KEGG: PANK2
	REACTOME: PANK2
	ConsensusPathDB
	Pathway Commons: PANK2
Metabolism	MetaCyc: PANK2
	HUMANCyc: PANK2
Regulation	Ensembl's Regulation: ENSG00000125779
	miRBase: chr20 :3,869,485-3,904,502
	TargetScan: NM_024960
	cisRED: ENSG00000125779
Context	iHOP: PANK2
	cancer metabolism search in PubMed: PANK2
	UCL Cancer Institute: PANK2
Assigned class in ccmGDB	C

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Phenotypic Information for PANK2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PANK2
	Familial Cancer Database: PANK2

* 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: PANK2
	MedGen: PANK2 (Human Medical Genetics with Condition)
	ClinVar: PANK2
Phenotype	MGI: PANK2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PANK2

Mutations for PANK2

* 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	PANK2	chr20	3873922	3873942	SULF2	chr20	46378455	46378475
ovary	PANK2	chr20	3876423	3876443	PANK2	chr20	3877468	3877488
ovary	PANK2	chr20	3884412	3884432	ATRN	chr20	3554091	3554111

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 PANK2 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
AI340170	PANK2	1	77	20	3870281	3870357	PANK2	73	288	20	3893104	3897611
BF896192	PANK2	1	252	20	3870508	3870763	VAMP3	253	388	1	7839660	7839795
BF354688	EPS15L1	13	152	19	16479453	16479592	PANK2	145	233	20	3903708	3903796
BF375856	PANK2	105	228	20	3873479	3873602	ACACB	211	392	12	109625921	109629547

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

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
chr20:3870079-3870079	p.L111Q	3
chr20:3870124-3870124	p.G126A	3
chr20:3888723-3888723	p.S260F	3
chr20:3869922-3869922	p.R59G	2
chr20:3891387-3891387	p.P382L	2
chr20:3903938-3903938	p.P570P	1
chr20:3888748-3888748	p.L268L	1
chr20:3891356-3891356	p.C372fs*8	1
chr20:3897581-3897581	p.N474H	1
chr20:3888790-3888790	p.L282L	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	6	1		4			1		3			4					3	2		8
# mutation	6	1		4			1		3			5					3	3		9
nonsynonymous SNV	3	1		1			1		3			5					2	2		6
synonymous SNV	3			3													1	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
chr20:3888790	p.L282L	2
chr20:3891319	p.F4C,PANK2	1
chr20:3897637	p.A201A,PANK2	1
chr20:3888593	p.S14S,PANK2	1
chr20:3891387	p.N236H,PANK2	1
chr20:3899360	p.E47K,PANK2	1
chr20:3888735	p.S251F,PANK2	1
chr20:3891416	p.L51L,PANK2	1
chr20:3899406	p.G253A,PANK2	1
chr20:3888740	p.S21F	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 PANK2 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 PANK2

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


ATRN,AP5S1,TMEM230,CDS2,CSNK2A1,CSNK2A3,FASTKD5, IDH3B,MAVS,MKKS,NOP56,PANK2,PCNA,PSMF1, PTPRA,RNF24,SRXN1,STK35,TBC1D20,ZCCHC3,ZNF343	ADH5,ARL6IP1,ATP5EP2,SMIM7,TMEM230,DNAJC25,FAIM, FAM45A,FNTA,GTF2E2,HNMT,HSD17B4,LOC729678,NUDT5, PANK2,RDH8,RNF130,RNF135,SNX5,SSB,UBXN8

ANKEF1,AP5S1,CDS2,CENPB,CSNK2A1,CSNK2A3,ESF1, FKBP1A,IDH3B,MKKS,NOP56,NSFL1C,PANK2,PSMF1, PTPRA,STK35,TASP1,TBC1D20,TRMT6,UBOX5,ZCCHC3	BCAS4,GDPGP1,CSK,CSNK2A1,DCP2,DERL1,DNAJC7, MBD2,NSF,NUMB,NUP50,PANK2,PIGR,PRKD2, PRR5L,SH3BP1,VCPIP1,VOPP1,WDFY1,ZNF217,ZNF490

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 PANK2

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
DB00151	pantothenate kinase 2	approved; nutraceutical	L-Cysteine

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Cross referenced IDs for PANK2

* 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