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 PROS1
Basic gene info.Gene symbolPROS1
Gene nameprotein S (alpha)
SynonymsPROS|PS21|PS22|PS23|PS24|PS25|PSA|THPH5|THPH6
CytomapUCSC genome browser: 3q11.2
Genomic locationchr3 :93591880-93692934
Type of geneprotein-coding
RefGenesNM_000313.3,
Ensembl idENSG00000184500
Descriptionprotein Savitamin K-dependent plasma protein Svitamin K-dependent protein S
Modification date20141207
dbXrefs MIM : 176880
HGNC : HGNC
Ensembl : ENSG00000184500
HPRD : 01473
Vega : OTTHUMG00000150354
ProteinUniProt: P07225
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PROS1
BioGPS: 5627
Gene Expression Atlas: ENSG00000184500
The Human Protein Atlas: ENSG00000184500
PathwayNCI Pathway Interaction Database: PROS1
KEGG: PROS1
REACTOME: PROS1
ConsensusPathDB
Pathway Commons: PROS1
MetabolismMetaCyc: PROS1
HUMANCyc: PROS1
RegulationEnsembl's Regulation: ENSG00000184500
miRBase: chr3 :93,591,880-93,692,934
TargetScan: NM_000313
cisRED: ENSG00000184500
ContextiHOP: PROS1
cancer metabolism search in PubMed: PROS1
UCL Cancer Institute: PROS1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PROS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PROS1
Familial Cancer Database: PROS1
* 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_PROTEINS

check002.gifOthers
OMIM 176880; gene.
612336; phenotype.
614514; phenotype.
Orphanet 743; Hereditary thrombophilia due to congenital protein S deficiency.
DiseaseKEGG Disease: PROS1
MedGen: PROS1 (Human Medical Genetics with Condition)
ClinVar: PROS1
PhenotypeMGI: PROS1 (International Mouse Phenotyping Consortium)
PhenomicDB: PROS1

Mutations for PROS1
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryPROS1chr39364795693647976PROS1chr39364812893648148
ovaryPROS1chr39367615193676171chr37375382273753842
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 PROS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE185151SDC11218022040190120402069PROS117643339362882293629079
AW579277PROS1123739367872793678963GLUL2312941182353484182353547

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 # sample1       1        
GAIN (# sample)1       1        
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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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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=111)
Stat. for Synonymous SNVs
(# total SNVs=22)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr3:93615439-93615439p.R316C5
chr3:93646100-93646100p.P76P3
chr3:93619656-93619656p.S240Y2
chr3:93595919-93595919p.S587S2
chr3:93598096-93598096p.G519S2
chr3:93603584-93603584p.H494Y2
chr3:93617331-93617331p.K270N2
chr3:93611944-93611944p.R330W2
chr3:93619687-93619687p.E230K2
chr3:93624637-93624637p.D198Y2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample41 122 4 22 2172 11311117
# mutation41 152 4 22 2472 11311124
nonsynonymous SNV41 111 4 22 2152 1127118
synonymous SNV   41      32   14 6
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
chr3:93598107p.R316C3
chr3:93615439p.R515H3
chr3:93617331p.K270N2
chr3:93646100p.P76P2
chr3:93595919p.S587S2
chr3:93595945p.N177N1
chr3:93611862p.G638G1
chr3:93619740p.V87I1
chr3:93646189p.R515C1
chr3:93603605p.E417Q1

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 PROS1 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 PROS1

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

ABCA6,ARHGAP20,CAV1,COL14A1,ERG,FAM126A,FAT4,
FOXO1,FREM1,JAM2,KCTD12,LHFP,LPCAT2,MYLK,
PKD2,PLSCR4,PROS1,RHOJ,SPARCL1,TNS1,TSHZ2
AKT3,ANTXR1,CALD1,CTSK,CTSO,CXCL12,DCN,
DPYSL2,FKBP7,IFI16,IL33,NT5E,OGN,OMD,
PDCD1LG2,PDGFD,PROS1,PTGFR,SGCE,TFPI,UST

ARL13B,BBS9,BBX,DYNC2H1,FOXO1,GNB5,GPR137B,
HINT3,NAV1,PAM,PLEKHA4,PLSCR4,PROS1,PRRG1,
RNF144B,SDCBP,SERINC1,SHISA2,SNPH,TMEM233,TMOD2
C10orf120,IZUMO2,TDRP,CELA2B,CGB2,COX7B2,FAM153B,
GJA10,GNA14,KCTD12,LRRC36,MC2R,OPN1LW,PDP1,
PROP1,PROS1,SLITRK5,SNORA38B,TDRD1,UTS2,WFDC6
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 PROS1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA33809; -.
Organism-specific databasesCTD 5627; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00170protein S (alpha)approved; nutraceuticalMenadione
DB00464protein S (alpha)approvedSodium Tetradecyl Sulfate
DB00682protein S (alpha)approvedWarfarin


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Cross referenced IDs for PROS1
* 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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