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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RPL39 |
Basic gene info. | Gene symbol | RPL39 |
Gene name | ribosomal protein L39 | |
Synonyms | L39|RPL39P42|RPL39_23_1806 | |
Cytomap | UCSC genome browser: Xq24 | |
Genomic location | chrX :118920468-118925606 | |
Type of gene | protein-coding | |
RefGenes | NM_001000.3, | |
Ensembl id | ENSG00000198918 | |
Description | 60S ribosomal protein L39 | |
Modification date | 20141222 | |
dbXrefs | MIM : 300899 | |
HGNC : HGNC | ||
Ensembl : ENSG00000198918 | ||
HPRD : 03546 | ||
Vega : OTTHUMG00000022278 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RPL39 | |
BioGPS: 6170 | ||
Gene Expression Atlas: ENSG00000198918 | ||
The Human Protein Atlas: ENSG00000198918 | ||
Pathway | NCI Pathway Interaction Database: RPL39 | |
KEGG: RPL39 | ||
REACTOME: RPL39 | ||
ConsensusPathDB | ||
Pathway Commons: RPL39 | ||
Metabolism | MetaCyc: RPL39 | |
HUMANCyc: RPL39 | ||
Regulation | Ensembl's Regulation: ENSG00000198918 | |
miRBase: chrX :118,920,468-118,925,606 | ||
TargetScan: NM_001000 | ||
cisRED: ENSG00000198918 | ||
Context | iHOP: RPL39 | |
cancer metabolism search in PubMed: RPL39 | ||
UCL Cancer Institute: RPL39 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RPL39(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: RPL39 |
Familial Cancer Database: RPL39 |
* 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_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: RPL39 |
MedGen: RPL39 (Human Medical Genetics with Condition) | |
ClinVar: RPL39 | |
Phenotype | MGI: RPL39 (International Mouse Phenotyping Consortium) |
PhenomicDB: RPL39 |
Mutations for RPL39 |
* 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 RPL39 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 |
BF848943 | FKTN | 5 | 357 | 9 | 108401945 | 108402299 | RPL39 | 350 | 429 | X | 118920542 | 118920621 |
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=6) | (# total SNVs=3) |
(# 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 |
chr23:118923917-118923917 | p.R21C | 3 |
chr23:118923947-118923947 | p.R11R | 1 |
chr23:118920674-118920674 | p.H43Q | 1 |
chr23:118923897-118923897 | p.I27I | 1 |
chr23:118923899-118923899 | p.I27V | 1 |
chr23:118923906-118923906 | p.P24P | 1 |
chr23:118923932-118923932 | p.K16E | 1 |
chr23:118923942-118923942 | p.F12F | 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 |   |   |   | 4 |   |   | 1 |   |   |   |   |   |   |   |   |   | 2 |   |   | 6 |
# mutation |   |   |   | 3 |   |   | 1 |   |   |   |   |   |   |   |   |   | 2 |   |   | 5 |
nonsynonymous SNV |   |   |   | 2 |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   | 3 |
synonymous SNV |   |   |   | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   | 1 |   |   | 2 |
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 |
chrX:118923917 | p.R21S | 4 |
chrX:118923932 | p.H43Q | 1 |
chrX:118923942 | p.R42R | 1 |
chrX:118923947 | p.M29I | 1 |
chrX:118920674 | p.I27I | 1 |
chrX:118920677 | p.I27V | 1 |
chrX:118923891 | p.P24P | 1 |
chrX:118923897 | p.K16E | 1 |
chrX:118923899 | p.F12F | 1 |
chrX:118923906 | p.R11R | 1 |
Other DBs for Point Mutations |
Copy Number for RPL39 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 RPL39 |
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 |
NDUFA1,RPL13,RPL14,RPL18,RPL24,RPL27A,RPL32, RPL35,RPL35A,RPL37,RPL37A,RPL38,RPL39,RPLP1, RPLP2,RPS11,RPS17,RPS18,RPS19,RPS2,RPS7 | METTL23,C18orf21,CAMLG,COMMD6,DUT,EIF3M,EXOSC8, LSM5,RPL15,RPL22L1,RPL23A,RPL30,RPL32,RPL34, RPL39,RPS12,RPS13,RSL24D1,SNRPE,TIMM9,UXT |
ATP5EP2,IGBP1P1,DUX4,HIST1H4K,LOC653544,FTX,PPIAL4G, RPL13AP20,RPL13AP6,RPL21,RPL36A,RPL39,RPS26P11,RPSAP9, TBC1D3P2,TPI1P3,Z | ACOT13,C2orf47,COX16,COX5A,DHRS7B,EAPP,H3F3A, HSD17B8,MAT2B,RPL36,RPL37A,RPL39,RPLP2,RPS29, SDHD,SFT2D1,TMEM179B,TMEM60,UQCRH,UQCRHL,UXT |
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 RPL39 |
There's no related Drug. |
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Cross referenced IDs for RPL39 |
* 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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