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 PCSK1
Basic gene info.Gene symbolPCSK1
Gene nameproprotein convertase subtilisin/kexin type 1
SynonymsBMIQ12|NEC1|PC1|PC3|SPC3
CytomapUCSC genome browser: 5q15-q21
Genomic locationchr5 :95726039-95767863
Type of geneprotein-coding
RefGenesNM_000439.4,
NM_001177875.1,NM_001177876.1,
Ensembl idENSG00000175426
Descriptionneuroendocrine convertase 1prohormone convertase 1prohormone convertase 3
Modification date20141207
dbXrefs MIM : 162150
HGNC : HGNC
Ensembl : ENSG00000175426
HPRD : 01201
Vega : OTTHUMG00000122089
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PCSK1
BioGPS: 5122
Gene Expression Atlas: ENSG00000175426
The Human Protein Atlas: ENSG00000175426
PathwayNCI Pathway Interaction Database: PCSK1
KEGG: PCSK1
REACTOME: PCSK1
ConsensusPathDB
Pathway Commons: PCSK1
MetabolismMetaCyc: PCSK1
HUMANCyc: PCSK1
RegulationEnsembl's Regulation: ENSG00000175426
miRBase: chr5 :95,726,039-95,767,863
TargetScan: NM_000439
cisRED: ENSG00000175426
ContextiHOP: PCSK1
cancer metabolism search in PubMed: PCSK1
UCL Cancer Institute: PCSK1
Assigned class in ccmGDBC

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Phenotypic Information for PCSK1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PCSK1
Familial Cancer Database: PCSK1
* 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_AMINO_ACIDS_AND_DERIVATIVES
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PCSK1
MedGen: PCSK1 (Human Medical Genetics with Condition)
ClinVar: PCSK1
PhenotypeMGI: PCSK1 (International Mouse Phenotyping Consortium)
PhenomicDB: PCSK1

Mutations for PCSK1
* 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
pancreasPCSK1chr59576469595764715PCSK1chr59576497595764995
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 PCSK1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU948504PCSK1835759574803195759036TADA3356437398216539821734
CV313519PCSK1405959575147195751490EPCAM5014524760612047606930

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=68)
Stat. for Synonymous SNVs
(# total SNVs=25)
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
chr5:95746650-95746650p.G308E3
chr5:95733122-95733122p.G547D3
chr5:95746544-95746544p.Y343Y3
chr5:95757642-95757642p.D188N3
chr5:95728961-95728961p.R669Q3
chr5:95743998-95743998p.T375T3
chr5:95759067-95759067p.V165I3
chr5:95735774-95735774p.R438Q2
chr5:95757591-95757591p.E205K2
chr5:95735803-95735803p.K428N2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 17  4 32 652  225314
# mutation22 14  4 32 652  235320
nonsynonymous SNV1  12  3 22 441  145213
synonymous SNV12 2  1 1  211  9 17
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
chr5:95757642p.D188N,PCSK13
chr5:95759067p.V165I,PCSK13
chr5:95748167p.G308E,PCSK12
chr5:95746650p.F303F,PCSK12
chr5:95761603p.E106G,PCSK12
chr5:95746664p.T246M,PCSK12
chr5:95751821p.G209W,PCSK12
chr5:95746673p.G652G,PCSK11
chr5:95730722p.A453V,PCSK11
chr5:95735729p.R312C,PCSK11

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 PCSK1 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 PCSK1

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

ADCYAP1,APLP1,DDX25,UNC79,MGAT5B,MMP26,NTRK2,
NTS,P2RX6,PCSK1,PRMT8,PSD,PTPRN,RTBDN,
RUNDC3A,SCG3,SNAP25,SYP,SYT4,TMEM145,UNC13A
ACTL6B,CARTPT,CHRNB4,CPLX2,EPYC,FLJ36000,GIP,
HMP19,IBSP,IFNA14,LCE2D,LOC650293,LOC729121,LOC732275,
NEU2,OR8B2,OR8H3,PCSK1,SEZ6,SYT4,TRIM48

C15orf26,LINC00261,CCDC174,CA8,CCDC60,CIB4,FZD9,
GALNT8,KIAA1324,KIF19,KLK12,MESDC1,NEURL1,OPRD1,
PCSK1,RAP1GAP,RHBDL3,SERPINA1,SLC18A1,SMAD9,PRSS3P2
AVPR1B,C17orf105,C17orf77,CELSR1,CFC1B,CYP2W1,FMOD,
HOXD12,INSL5,NKX2-2,NKX2-8,PCSK1,PPY2,PRB4,
SCG5,SLC18A1,SLC38A11,TBX4,TNNC1,TPH1,TUSC3
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 PCSK1


There's no related Drug.
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Cross referenced IDs for PCSK1
* 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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