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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PRELP |
Basic gene info. | Gene symbol | PRELP |
Gene name | proline/arginine-rich end leucine-rich repeat protein | |
Synonyms | MST161|MSTP161|SLRR2A | |
Cytomap | UCSC genome browser: 1q32 | |
Genomic location | chr1 :203444882-203460479 | |
Type of gene | protein-coding | |
RefGenes | NM_002725.3, NM_201348.1, | |
Ensembl id | ENSG00000188783 | |
Description | 55 kDa leucine-rich repeat protein of articular cartilageprolarginprolargin proteoglycanproline-arginine-rich end leucine-rich repeat protein | |
Modification date | 20141207 | |
dbXrefs | MIM : 601914 | |
HGNC : HGNC | ||
Ensembl : ENSG00000188783 | ||
HPRD : 03556 | ||
Vega : OTTHUMG00000035911 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PRELP | |
BioGPS: 5549 | ||
Gene Expression Atlas: ENSG00000188783 | ||
The Human Protein Atlas: ENSG00000188783 | ||
Pathway | NCI Pathway Interaction Database: PRELP | |
KEGG: PRELP | ||
REACTOME: PRELP | ||
ConsensusPathDB | ||
Pathway Commons: PRELP | ||
Metabolism | MetaCyc: PRELP | |
HUMANCyc: PRELP | ||
Regulation | Ensembl's Regulation: ENSG00000188783 | |
miRBase: chr1 :203,444,882-203,460,479 | ||
TargetScan: NM_002725 | ||
cisRED: ENSG00000188783 | ||
Context | iHOP: PRELP | |
cancer metabolism search in PubMed: PRELP | ||
UCL Cancer Institute: PRELP | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PRELP(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PRELP |
Familial Cancer Database: PRELP |
* This gene is included in those cancer gene databases. |
. | ||||||||||||||||||||
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_CARBOHYDRATES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PRELP |
MedGen: PRELP (Human Medical Genetics with Condition) | |
ClinVar: PRELP | |
Phenotype | MGI: PRELP (International Mouse Phenotyping Consortium) |
PhenomicDB: PRELP |
Mutations for PRELP |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PRELP 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 |
BU727928 | CCDC36 | 1 | 321 | 3 | 49282867 | 49283627 | PRELP | 313 | 475 | 1 | 203452298 | 203452459 | |
BQ183043 | PRELP | 14 | 573 | 1 | 203453183 | 203456291 | LOC100507412 | 571 | 671 | ? | 110051 | 110152 | |
BM686368 | PRELP | 8 | 307 | 1 | 203444931 | 203452459 | CCDC36 | 299 | 567 | 3 | 49282867 | 49283136 | |
DA313778 | LIPA | 1 | 135 | 10 | 90977996 | 90978130 | PRELP | 128 | 525 | 1 | 203458346 | 203458743 | |
BF986263 | CHD4 | 9 | 132 | 12 | 6709750 | 6710130 | PRELP | 125 | 271 | 1 | 203452442 | 203452588 |
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=49) | (# total SNVs=23) |
(# total SNVs=0) | (# 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 |
chr1:203453021-203453021 | p.P237S | 4 |
chr1:203452913-203452913 | p.D201Y | 2 |
chr1:203452395-203452395 | p.P28H | 2 |
chr1:203455833-203455833 | p.? | 2 |
chr1:203452538-203452538 | p.E76K | 2 |
chr1:203455842-203455842 | p.G328R | 2 |
chr1:203453245-203453245 | p.N311K | 2 |
chr1:203455873-203455873 | p.A338V | 2 |
chr1:203453266-203453266 | p.L318L | 2 |
chr1:203452389-203452389 | p.P26Q | 1 |
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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 | 1 | 2 | 1 | 11 |   |   | 3 |   | 2 | 1 | 1 | 12 | 5 | 3 |   |   | 3 | 3 |   | 10 |
# mutation | 1 | 2 | 1 | 10 |   |   | 3 |   | 2 | 1 | 1 | 11 | 5 | 3 |   |   | 3 | 3 |   | 10 |
nonsynonymous SNV |   | 1 | 1 | 5 |   |   | 3 |   | 1 | 1 |   | 7 | 3 | 2 |   |   | 2 | 2 |   | 7 |
synonymous SNV | 1 | 1 |   | 5 |   |   |   |   | 1 |   | 1 | 4 | 2 | 1 |   |   | 1 | 1 |   | 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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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 |
chr1:203453266 | p.L318L,PRELP | 2 |
chr1:203455927 | p.D201Y,PRELP | 2 |
chr1:203455928 | p.R356Q,PRELP | 2 |
chr1:203452913 | p.R356R,PRELP | 2 |
chr1:203452396 | p.D369G,PRELP | 1 |
chr1:203453253 | p.P28P,PRELP | 1 |
chr1:203452734 | p.R171Q,PRELP | 1 |
chr1:203455883 | p.E314G,PRELP | 1 |
chr1:203453017 | p.V381V,PRELP | 1 |
chr1:203452401 | p.T30I,PRELP | 1 |
Other DBs for Point Mutations |
Copy Number for PRELP 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 PRELP |
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 |
ACAN,BGN,NPR3,ENPEP,EXT2,FOLR1,FRZB, FXYD4,MIA,NOS2,NPR2,PANX3,PHOSPHO1,PRELP, PRSS54,S100A1,SCRG1,SLC6A18,SNAI2,TTYH1,WWP2 | ABCA8,ALDH2,ANTXR2,LINC00341,C1QTNF1,CDKN2B,CRTAP, DUSP22,EBF3,FYN,GABARAPL1,GALNT15,GSN,KANK2, NDRG1,PCOLCE2,PRELP,SLC9A9,TBC1D2B,TMBIM1,VIM |
AOC3,BOC,CDO1,CPXM2,EFEMP1,FBLN5,FHL1, GPIHBP1,LHFP,MGP,PODN,PRELP,PTGIS,PTH1R, RBMS3,RNF180,SLIT2,SLIT3,STON1,TCF7L1,TMEM130 | ADAMTSL3,BOC,CC2D2A,CD81,CLIP3,DIP2C,FGFR1, GLI3,GPRASP1,GRIK5,MID2,NPR2,PDE2A,PEG3, PRELP,PTPRM,SCN2B,SLC29A1,SMARCA1,TIMP2,ZNF532 |
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 PRELP |
There's no related Drug. |
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Cross referenced IDs for PRELP |
* 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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