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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PCSK1 |
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Phenotypic Information for PCSK1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PCSK1 |
Familial Cancer Database: PCSK1 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_INTEGRATION_OF_ENERGY_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PCSK1 |
MedGen: PCSK1 (Human Medical Genetics with Condition) | |
ClinVar: PCSK1 | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | PCSK1 | chr5 | 95764695 | 95764715 | PCSK1 | chr5 | 95764975 | 95764995 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PCSK1 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BU948504 | PCSK1 | 8 | 357 | 5 | 95748031 | 95759036 | TADA3 | 356 | 437 | 3 | 9821653 | 9821734 | |
CV313519 | PCSK1 | 40 | 59 | 5 | 95751471 | 95751490 | EPCAM | 50 | 145 | 2 | 47606120 | 47606930 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=68) | (# total SNVs=25) |
(# total SNVs=2) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr5:95728961-95728961 | p.R669Q | 3 |
chr5:95743998-95743998 | p.T375T | 3 |
chr5:95759067-95759067 | p.V165I | 3 |
chr5:95746650-95746650 | p.G308E | 3 |
chr5:95733122-95733122 | p.G547D | 3 |
chr5:95746544-95746544 | p.Y343Y | 3 |
chr5:95757642-95757642 | p.D188N | 3 |
chr5:95757660-95757660 | p.D182N | 2 |
chr5:95746582-95746582 | p.I331V | 2 |
chr5:95761603-95761603 | p.E106G | 2 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 2 | 2 |   | 17 |   |   | 4 |   | 3 | 2 |   | 6 | 5 | 2 |   |   | 22 | 5 | 3 | 14 |
# mutation | 2 | 2 |   | 14 |   |   | 4 |   | 3 | 2 |   | 6 | 5 | 2 |   |   | 23 | 5 | 3 | 20 |
nonsynonymous SNV | 1 |   |   | 12 |   |   | 3 |   | 2 | 2 |   | 4 | 4 | 1 |   |   | 14 | 5 | 2 | 13 |
synonymous SNV | 1 | 2 |   | 2 |   |   | 1 |   | 1 |   |   | 2 | 1 | 1 |   |   | 9 |   | 1 | 7 |
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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr5:95757642 | p.D188N,PCSK1 | 3 |
chr5:95759067 | p.V165I,PCSK1 | 3 |
chr5:95748167 | p.E106G,PCSK1 | 2 |
chr5:95746650 | p.T246M,PCSK1 | 2 |
chr5:95761603 | p.G209W,PCSK1 | 2 |
chr5:95746664 | p.G308E,PCSK1 | 2 |
chr5:95751821 | p.F303F,PCSK1 | 2 |
chr5:95734656 | p.I695I,PCSK1 | 1 |
chr5:95748142 | p.E540K,PCSK1 | 1 |
chr5:95728867 | p.T377M,PCSK1 | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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