Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolPANK2
Gene namepantothenate kinase 2
SynonymsC20orf48|HARP|HSS|NBIA1|PKAN
CytomapUCSC genome browser: 20p13
Genomic locationchr20 :3869485-3904502
Type of geneprotein-coding
RefGenesNM_024960.4,
NM_153638.2,NM_153640.2,NM_153637.1,NM_153639.1,
NM_153641.1,
Ensembl idENSG00000125779
DescriptionHallervorden-Spatz syndromepantothenate kinase 2, mitochondrialpantothenic acid kinase 2
Modification date20141219
dbXrefs MIM : 606157
HGNC : HGNC
Ensembl : ENSG00000125779
Vega : OTTHUMG00000031768
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PANK2
BioGPS: 80025
Gene Expression Atlas: ENSG00000125779
The Human Protein Atlas: ENSG00000125779
PathwayNCI Pathway Interaction Database: PANK2
KEGG: PANK2
REACTOME: PANK2
ConsensusPathDB
Pathway Commons: PANK2
MetabolismMetaCyc: PANK2
HUMANCyc: PANK2
RegulationEnsembl's Regulation: ENSG00000125779
miRBase: chr20 :3,869,485-3,904,502
TargetScan: NM_024960
cisRED: ENSG00000125779
ContextiHOP: PANK2
cancer metabolism search in PubMed: PANK2
UCL Cancer Institute: PANK2
Assigned class in ccmGDBC

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Phenotypic Information for PANK2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PANK2
MedGen: PANK2 (Human Medical Genetics with Condition)
ClinVar: PANK2
PhenotypeMGI: PANK2 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPANK2chr2038739223873942SULF2chr204637845546378475
ovaryPANK2chr2038764233876443PANK2chr2038774683877488
ovaryPANK2chr2038844123884432ATRNchr2035540913554111
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PANK2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI340170PANK21772038702813870357PANK2732882038931043897611
BF896192PANK212522038705083870763VAMP3253388178396607839795
BF354688EPS15L113152191647945316479592PANK21452332039037083903796
BF375856PANK21052282038734793873602ACACB21139212109625921109629547

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr20:3870079-3870079p.L111Q3
chr20:3870124-3870124p.G126A3
chr20:3888723-3888723p.S260F3
chr20:3869922-3869922p.R59G2
chr20:3891387-3891387p.P382L2
chr20:3888740-3888740p.V266M1
chr20:3899434-3899434p.S551S1
chr20:3891319-3891319p.Q359Q1
chr20:3869920-3869920p.P58L1
chr20:3897573-3897573p.?1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample61 4  1 3  4    32 8
# mutation61 4  1 3  5    33 9
nonsynonymous SNV31 1  1 3  5    22 6
synonymous SNV3  3            11 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr20:3888790p.L282L2
chr20:3891288p.L268L1
chr20:3897586p.N183H,PANK21
chr20:3870338p.M184I,PANK21
chr20:3891319p.F4C,PANK21
chr20:3897637p.A201A,PANK21
chr20:3888593p.S14S,PANK21
chr20:3891387p.N236H,PANK21
chr20:3899360p.E47K,PANK21
chr20:3888735p.S251F,PANK21

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00151pantothenate kinase 2approved; nutraceuticalL-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



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