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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RPS23 |
Basic gene info. | Gene symbol | RPS23 |
Gene name | ribosomal protein S23 | |
Synonyms | S23 | |
Cytomap | UCSC genome browser: 5q14.2 | |
Genomic location | chr5 :81569138-81574235 | |
Type of gene | protein-coding | |
RefGenes | NM_001025.4, | |
Ensembl id | ENSG00000186468 | |
Description | 40S ribosomal protein S23homolog of yeast ribosomal protein S28 | |
Modification date | 20141207 | |
dbXrefs | MIM : 603683 | |
HGNC : HGNC | ||
Ensembl : ENSG00000186468 | ||
HPRD : 04729 | ||
Vega : OTTHUMG00000162557 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RPS23 | |
BioGPS: 6228 | ||
Gene Expression Atlas: ENSG00000186468 | ||
The Human Protein Atlas: ENSG00000186468 | ||
Pathway | NCI Pathway Interaction Database: RPS23 | |
KEGG: RPS23 | ||
REACTOME: RPS23 | ||
ConsensusPathDB | ||
Pathway Commons: RPS23 | ||
Metabolism | MetaCyc: RPS23 | |
HUMANCyc: RPS23 | ||
Regulation | Ensembl's Regulation: ENSG00000186468 | |
miRBase: chr5 :81,569,138-81,574,235 | ||
TargetScan: NM_001025 | ||
cisRED: ENSG00000186468 | ||
Context | iHOP: RPS23 | |
cancer metabolism search in PubMed: RPS23 | ||
UCL Cancer Institute: RPS23 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RPS23(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: RPS23 |
Familial Cancer Database: RPS23 |
* 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/ |
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REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: RPS23 |
MedGen: RPS23 (Human Medical Genetics with Condition) | |
ClinVar: RPS23 | |
Phenotype | MGI: RPS23 (International Mouse Phenotyping Consortium) |
PhenomicDB: RPS23 |
Mutations for RPS23 |
* 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 RPS23 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 |
AI908980 | RPS23 | 14 | 188 | 5 | 81573514 | 81574155 | RPS24 | 189 | 253 | 10 | 79799960 | 79800413 | |
BQ222647 | RPS23 | 1 | 497 | 5 | 81571879 | 81574158 | MRPL30 | 483 | 505 | 2 | 99879071 | 99879093 | |
BM785206 | TUBA1C | 4 | 389 | 12 | 49658867 | 49663672 | RPS23 | 383 | 455 | 5 | 81571883 | 81571955 | |
AI889745 | NLGN4X | 1 | 44 | X | 6143720 | 6143763 | RPS23 | 39 | 108 | 5 | 81571879 | 81571948 | |
BF154662 | SNX19 | 1 | 246 | 11 | 130750593 | 130753340 | RPS23 | 238 | 380 | 5 | 81572280 | 81573597 | |
CB217558 | MRPL30 | 21 | 43 | 2 | 99879071 | 99879093 | RPS23 | 29 | 345 | 5 | 81571879 | 81572337 | |
CA429429 | RPS23 | 13 | 85 | 5 | 81571879 | 81571951 | CCDC80 | 83 | 596 | 3 | 112358666 | 112359590 | |
AI982804 | EFNA5 | 1 | 137 | 5 | 106713905 | 106714041 | RPS23 | 124 | 486 | 5 | 81571295 | 81571656 | |
H17554 | CUTA | 1 | 117 | 6 | 4865649 | 4866157 | RPS23 | 101 | 505 | 5 | 81569969 | 81570373 |
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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=1) | (# total SNVs=10) |
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(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr5:81573670-81573670 | p.G34G | 6 |
chr5:81574149-81574149 | p.A30A | 1 |
chr5:81572042-81572042 | p.G138G | 1 |
chr5:81572228-81572228 | p.N124H | 1 |
chr5:81572316-81572316 | p.P94P | 1 |
chr5:81573514-81573514 | p.K86K | 1 |
chr5:81573573-81573573 | p.A67T | 1 |
chr5:81573622-81573622 | p.R50R | 1 |
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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 | 5 |   |   |   |   |   |   |   |   |   |   |   |   |   | 2 |   | 1 |
# mutation |   |   | 2 | 5 |   |   |   |   |   |   |   |   |   |   |   |   |   | 2 |   | 1 |
nonsynonymous SNV |   |   | 1 | 4 |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |
synonymous SNV |   |   | 1 | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   | 1 |
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 |
chr5:81573560 | p.G33D | 1 |
chr5:81573573 | p.R18R | 1 |
chr5:81573578 | p.G106G | 1 |
chr5:81573622 | p.V85L | 1 |
chr5:81572042 | p.G78D | 1 |
chr5:81572249 | p.P62P | 1 |
chr5:81572269 | p.I50I | 1 |
chr5:81572316 | p.H46Y | 1 |
chr5:81573526 | p.N39T | 1 |
chr5:81573540 | p.A35T | 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 RPS23 |
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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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GNB2L1,HNRNPA1,NACA,RPL10,RPL10A,RPL11,RPL14, RPL15,RPL26,RPL29,RPL31,RPL32,RPL34,RPL37A, RPL6,RPL7A,RPS13,RPS14,RPS23,RPS4X,RPS8 | EEF1B2,RPL10,RPL14,RPL22,RPL24,RPL30,RPL31, RPL32,RPL35A,RPL37,RPL38,RPL41,RPL4,RPL5, RPL6,RPS12,RPS23,RPS27A,RPS3A,RPS6,RPS7 |
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BTF3,GNB2L1,RPL10A,RPL12,RPL14,RPL15,RPL29, RPL31,RPL32,RPL35A,RPL36,RPL37,RPL37A,RPL5, RPL7A,RPS13,RPS14,RPS23,RPS6,RPS8,RPS9 | EEF1A1,RPL10,RPL12,RPL15,RPL19,RPL30,RPL32, RPL35A,RPL3,RPL38,RPL41,RPL6,RPL7A,RPLP1, RPS11,RPS12,RPS13,RPS23,RPS25,RPS3,RPS9 |
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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 RPS23 |
There's no related Drug. |
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Cross referenced IDs for RPS23 |
* 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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