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 PAPSS2
Basic gene info.Gene symbolPAPSS2
Gene name3'-phosphoadenosine 5'-phosphosulfate synthase 2
SynonymsATPSK2|BCYM4|SK2
CytomapUCSC genome browser: 10q24
Genomic locationchr10 :89419475-89507462
Type of geneprotein-coding
RefGenesNM_001015880.1,
NM_004670.3,
Ensembl idENSG00000198682
Description3-prime-phosphoadenosine 5-prime-phosphosulfate synthase 2ATP sulfurylase/APS kinase 2ATP sulfurylase/adenosine 5'-phosphosulfate kinasePAPS synthase 2PAPS synthetase 2SK 2bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2bifunctional 3'
Modification date20141207
dbXrefs MIM : 603005
HGNC : HGNC
Ensembl : ENSG00000198682
HPRD : 04303
Vega : OTTHUMG00000018683
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PAPSS2
BioGPS: 9060
Gene Expression Atlas: ENSG00000198682
The Human Protein Atlas: ENSG00000198682
PathwayNCI Pathway Interaction Database: PAPSS2
KEGG: PAPSS2
REACTOME: PAPSS2
ConsensusPathDB
Pathway Commons: PAPSS2
MetabolismMetaCyc: PAPSS2
HUMANCyc: PAPSS2
RegulationEnsembl's Regulation: ENSG00000198682
miRBase: chr10 :89,419,475-89,507,462
TargetScan: NM_001015880
cisRED: ENSG00000198682
ContextiHOP: PAPSS2
cancer metabolism search in PubMed: PAPSS2
UCL Cancer Institute: PAPSS2
Assigned class in ccmGDBC

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Phenotypic Information for PAPSS2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PAPSS2
Familial Cancer Database: PAPSS2
* 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
KEGG_PURINE_METABOLISM
KEGG_SELENOAMINO_ACID_METABOLISM
KEGG_SULFUR_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PAPSS2
MedGen: PAPSS2 (Human Medical Genetics with Condition)
ClinVar: PAPSS2
PhenotypeMGI: PAPSS2 (International Mouse Phenotyping Consortium)
PhenomicDB: PAPSS2

Mutations for PAPSS2
* 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
ovaryPAPSS2chr108943215189432171PAPSS2chr108947504789475067
pancreasPAPSS2chr108942030789420327GRID1chr108812586488125884
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 PAPSS2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA149744PLEKHJ111091922331822233290PAPSS2108516108950624589506651

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample21311  4 2    33 1
GAIN (# sample)                 
LOSS (# sample)21311  4 2    33 1
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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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=34)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr10:89487102-89487102p.R309R2
chr10:89473069-89473069p.?2
chr10:89503327-89503327p.G469R2
chr10:89474550-89474550p.R190H2
chr10:89503286-89503286p.L455P1
chr10:89474556-89474556p.L192R1
chr10:89505676-89505676p.P598P1
chr10:89469019-89469019p.Q32*1
chr10:89501105-89501105p.Q395H1
chr10:89473067-89473067p.K127K1

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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
# sample22 53 2 32 7111 6518
# mutation22 62 2 32 9111 6519
nonsynonymous SNV   52 2 31 7111 5416
synonymous SNV22 1     1 2    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
chr10:89475553p.R273Q,PAPSS22
chr10:89474814p.H24N,PAPSS21
chr10:89501012p.S180S,PAPSS21
chr10:89469058p.R309R,PAPSS21
chr10:89503313p.H570Y,PAPSS21
chr10:89473817p.R580Q,PAPSS21
chr10:89474820p.G42V,PAPSS21
chr10:89501052p.S197F,PAPSS21
chr10:89472834p.A331T,PAPSS21
chr10:89504826p.P598P,PAPSS21

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 PAPSS2 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 PAPSS2

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

ABCC4,ACSM1,C15orf43,CRH,ENPP3,GLYATL2,KMO,
KYNU,MPV17L,OR4A5,PAPSS2,SCP2,SERHL2,SERHL,
SLC38A4,SULT1C3,TAF1L,TMEM45B,TMEM62,TMIGD1,UGT3A2
ABHD6,ANO10,CCNYL1,CPPED1,CRK,ECM2,FAM173B,
FAR2,FBXW2,FITM2,GNS,ME1,NQO1,OSTM1,
PAPSS2,PARM1,PBLD,SEC22B,SLC5A3,TSKU,ZDHHC3

BCL10,C4orf19,CA12,CASP7,GNAQ,HK2,IQGAP2,
ITM2C,LIMA1,NR3C2,PAPSS2,PIGR,RBM47,RNF145,
SGMS2,SIAE,STYK1,TC2N,TNFRSF11A,TNFSF13,TSPAN1
ACOX1,ACSS2,ALAS1,ARF3,ATP1B1,CDH17,CDH1,
RHOV___CHP1,CORO2A,CUL3,IQGAP2,PAPSS2,PDCD6IP,PLD1,
RAB14,RBM47,SFXN1,SLC22A5,SLC41A2,STK38,UGT1A10
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 PAPSS2


There's no related Drug.
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Cross referenced IDs for PAPSS2
* 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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