Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 PAPSS1
Basic gene info.Gene symbolPAPSS1
Gene name3'-phosphoadenosine 5'-phosphosulfate synthase 1
SynonymsATPSK1|PAPSS|SK1
CytomapUCSC genome browser: 4q24
Genomic locationchr4 :108534821-108641419
Type of geneprotein-coding
RefGenesNM_005443.4,
Ensembl idENSG00000138801
Description3-prime-phosphoadenosine 5-prime-phosphosulfate synthase 1PAPS synthase 1PAPSS 1SK 1bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1sulfurylase kinase 1
Modification date20141207
dbXrefs MIM : 603262
HGNC : HGNC
Ensembl : ENSG00000138801
HPRD : 09132
Vega : OTTHUMG00000131210
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PAPSS1
BioGPS: 9061
Gene Expression Atlas: ENSG00000138801
The Human Protein Atlas: ENSG00000138801
PathwayNCI Pathway Interaction Database: PAPSS1
KEGG: PAPSS1
REACTOME: PAPSS1
ConsensusPathDB
Pathway Commons: PAPSS1
MetabolismMetaCyc: PAPSS1
HUMANCyc: PAPSS1
RegulationEnsembl's Regulation: ENSG00000138801
miRBase: chr4 :108,534,821-108,641,419
TargetScan: NM_005443
cisRED: ENSG00000138801
ContextiHOP: PAPSS1
cancer metabolism search in PubMed: PAPSS1
UCL Cancer Institute: PAPSS1
Assigned class in ccmGDBC

Top
Phenotypic Information for PAPSS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PAPSS1
Familial Cancer Database: PAPSS1
* 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: PAPSS1
MedGen: PAPSS1 (Human Medical Genetics with Condition)
ClinVar: PAPSS1
PhenotypeMGI: PAPSS1 (International Mouse Phenotyping Consortium)
PhenomicDB: PAPSS1

Mutations for PAPSS1
* 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
ovaryPAPSS1chr4108639417108639437PAPSS1chr4108639944108639964
pancreasPAPSS1chr4108592320108592340ACTN4chr193918834939188369
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 PAPSS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ302970PAPSS163564108581122108608320PKNOX1355379214445029244450316
AI499330PAPSS112304108535057108535286PAPSS12256024108535468108535845
CB216910PNKD13622219195404219195765PAPSS13586484108535341108552874
DA811913PAPSS11534108603212108603264RAB13545921153955055153958815

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample             1   
GAIN (# sample)                 
LOSS (# sample)             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)

Top
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=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=52)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr4:108574727-108574727p.R386Q4
chr4:108641317-108641317p.L7L4
chr4:108615003-108615003p.R112H3
chr4:108552981-108552981p.G514G2
chr4:108622324-108622324p.?2
chr4:108614998-108614998p.A114T2
chr4:108608287-108608287p.F153S2
chr4:108615079-108615079p.D87Y2
chr4:108575925-108575925p.F343V2
chr4:108603176-108603176p.E222K2

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 5  3 3  6 1  3718
# mutation 2 5  3 3  6 1  3718
nonsynonymous SNV 2 5  3 2  4 1  3517
synonymous SNV        1  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])

Top
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
chr4:108574727p.R386Q3
chr4:108566109p.N98N1
chr4:108578142p.K97T1
chr4:108535506p.R592C1
chr4:108615048p.T358T1
chr4:108566127p.R92H1
chr4:108581180p.R590Q1
chr4:108535511p.A312A1
chr4:108615063p.T66T1
chr4:108566169p.K569N1

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 PAPSS1 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]

Top
Gene Expression for PAPSS1

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ANP32E,ARHGEF9,DSC2,FAM171A1,FOXC1,GABRP,GPR125,
KIAA1804,MRAS,PAPSS1,PM20D2,RGMA,ROPN1,SFT2D2,
SOX10,SOX6,ST8SIA1,TBX19,TIGD2,TRIM2,UGT8
APP,FAM201A,CHMP4C,CTBP2,CTNNB1,DKC1,ESRP1,
GTF3C2,KDM1A,LRRC8D,NONO,PAPSS1,RFC5,SDR42E1,
SEMA4A,SEPHS1,SEPT3,SMARCC1,TDP1,VANGL2,VSNL1

ATP10D,C10orf10,CALHM2,CEP170,CTSO,FYN,GNB5,
KLHL2,LIX1L,MANBA,NCF2,NOTCH2,PAPSS1,PLSCR3,
PPP3CA,RAB8B,SEC24D,SGTB,SLC39A6,SRGAP2,TWSG1
ARMCX6,BBS10,BRF2,ARL14EP,FAM212A,ZBED8,FAM220A,
EFCAB7,MSANTD4,METTL6,PAIP2,PAPSS1,PEX12,POLR3GL,
RGS10,ZC3H10,ZFP82,ZNF134,ZNF14,ZNF501,ZNF691
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for PAPSS1
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
DB026613'-phosphoadenosine 5'-phosphosulfate synthase 1experimentalAdenosine-5'-Diphosphate-2',3'-Vanadate
DB034313'-phosphoadenosine 5'-phosphosulfate synthase 1experimentalAdenosine-5'-Diphosphate
DB037083'-phosphoadenosine 5'-phosphosulfate synthase 1experimentalAdenosine-5'-Phosphosulfate
DB040773'-phosphoadenosine 5'-phosphosulfate synthase 1experimentalGlycerol
DB007833'-phosphoadenosine 5'-phosphosulfate synthase 1approved; investigationalEstradiol


Top
Cross referenced IDs for PAPSS1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas