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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RPL5 |
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Phenotypic Information for RPL5(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: RPL5 |
Familial Cancer Database: RPL5 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in GBM 6, |
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, 6 http://www.sciencedirect.com/science/article/pii/S0092867413012087, 7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
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REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
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OMIM | 603634; gene. 612561; phenotype. |
Orphanet | 124; Blackfan-Diamond anemia. |
Disease | KEGG Disease: RPL5 |
MedGen: RPL5 (Human Medical Genetics with Condition) | |
ClinVar: RPL5 | |
Phenotype | MGI: RPL5 (International Mouse Phenotyping Consortium) |
PhenomicDB: RPL5 |
Mutations for RPL5 |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPL5 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 |
AI376067 | RPL5 | 10 | 80 | 1 | 93307408 | 93307478 | WDR76 | 72 | 325 | 15 | 44158338 | 44158591 | |
AI040133 | RPL5 | 1 | 244 | 1 | 93306111 | 93307480 | MINK1 | 235 | 342 | 17 | 4794810 | 4794917 | |
EL584993 | FAM50A | 188 | 212 | X | 153674180 | 153674204 | RPL5 | 194 | 642 | 1 | 93297594 | 93301795 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=34) | (# total SNVs=3) |
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(# total SNVs=7) | (# total SNVs=1) |
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* 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 |
chr1:93299194-93299197 | p.N57fs*12 | 3 |
chr1:93301796-93301796 | p.V125A | 2 |
chr1:93298990-93298990 | p.Y16* | 2 |
chr1:93303104-93303104 | p.Y207H | 2 |
chr1:93306176-93306176 | p.K258N | 2 |
chr1:93300390-93300390 | p.E82K | 2 |
chr1:93299188-93299188 | p.R54C | 2 |
chr1:93303161-93303161 | p.Y226H | 2 |
chr1:93301949-93301949 | p.S176fs*36 | 2 |
chr1:93298955-93298955 | p.K5* | 2 |
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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 |   | 4 | 2 |   |   |   |   |   |   | 1 | 2 |   |   | 1 | 4 | 1 |   | 8 |
# mutation |   | 1 |   | 3 | 2 |   |   |   |   |   |   | 1 | 2 |   |   | 1 | 4 | 1 |   | 9 |
nonsynonymous SNV |   | 1 |   | 3 | 2 |   |   |   |   |   |   | 1 | 2 |   |   | 1 | 3 | 1 |   | 7 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 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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* 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 |
chr1:93301796 | p.V125A | 2 |
chr1:93306176 | p.K258N | 2 |
chr1:93303039 | p.A97G | 1 |
chr1:93300426 | p.V231I | 1 |
chr1:93303099 | p.G102V | 1 |
chr1:93300436 | p.R248Q | 1 |
chr1:93303104 | p.T154I | 1 |
chr1:93300451 | p.K164N | 1 |
chr1:93303108 | p.G169V | 1 |
chr1:93303111 | p.S176N | 1 |
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* 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. |
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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 RPL5 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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EEF1B2,EEF1G,RPL10A,RPL11,RPL17,RPL22,RPL27A, RPL31,RPL32,RPL3,RPL4,RPL5,RPL6,RPS10, RPS18,RPS25,RPS27A,RPS4X,RPS6,RPS7,RPS8 | EEF1B2,GNB2L1,NACA,RPL10A,RPL12,RPL14,RPL22, RPL24,RPL32,RPL35A,RPL37,RPL4,RPL5,RPL6, RPS18,RPS27A,RPS3A,RPS4X,RPS6,RPS7,RPS8 | ||||
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DPH5,RPL10A,RPL12,RPL15,RPL24,RPL29,RPL32, RPL36,RPL37A,RPL5,RPS10,RPS13,RPS14,RPS15A, RPS18,RPS23,RPS29,RPS3,RPS6,RPS7,RPS8 | BOD1,C12orf57,EEF1A1P9,MED28,PFDN5,RPL10A,RPL15, RPL24,RPL35A,RPL41,RPL5,RPS11,RPS13,RPS3A, RPS5,RPS6,RPS7,RPS8,RSL24D1,TIMM9,ZFAND1 |
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* 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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Pharmacological Information for RPL5 |
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DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA34755; -. |
Organism-specific databases | CTD | 6125; -. |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB03721 | ribosomal protein L5 | experimental | O-Sialic Acid | ![]() | ![]() |
DB01033 | ribosomal protein L5 | approved | Mercaptopurine | ![]() | ![]() |
DB00563 | ribosomal protein L5 | approved | Methotrexate | ![]() | ![]() |
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Cross referenced IDs for RPL5 |
* 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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