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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RPL27A |
Basic gene info. | Gene symbol | RPL27A |
Gene name | ribosomal protein L27a | |
Synonyms | L27A | |
Cytomap | UCSC genome browser: 11p15 | |
Genomic location | chr11 :8703994-8711419 | |
Type of gene | protein-coding | |
RefGenes | NM_000990.4, NM_032650.1, | |
Ensembl id | ENSG00000166441 | |
Description | 60S ribosomal protein L27a | |
Modification date | 20141207 | |
dbXrefs | MIM : 603637 | |
HGNC : HGNC | ||
Ensembl : ENSG00000166441 | ||
HPRD : 04701 | ||
Vega : OTTHUMG00000165834 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RPL27A | |
BioGPS: 6157 | ||
Gene Expression Atlas: ENSG00000166441 | ||
The Human Protein Atlas: ENSG00000166441 | ||
Pathway | NCI Pathway Interaction Database: RPL27A | |
KEGG: RPL27A | ||
REACTOME: RPL27A | ||
ConsensusPathDB | ||
Pathway Commons: RPL27A | ||
Metabolism | MetaCyc: RPL27A | |
HUMANCyc: RPL27A | ||
Regulation | Ensembl's Regulation: ENSG00000166441 | |
miRBase: chr11 :8,703,994-8,711,419 | ||
TargetScan: NM_000990 | ||
cisRED: ENSG00000166441 | ||
Context | iHOP: RPL27A | |
cancer metabolism search in PubMed: RPL27A | ||
UCL Cancer Institute: RPL27A | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RPL27A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: RPL27A |
Familial Cancer Database: RPL27A |
* 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: RPL27A |
MedGen: RPL27A (Human Medical Genetics with Condition) | |
ClinVar: RPL27A | |
Phenotype | MGI: RPL27A (International Mouse Phenotyping Consortium) |
PhenomicDB: RPL27A |
Mutations for RPL27A |
* 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 |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
- 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 |
ovary | RPL27A | chr11 | 8710126 | 8710146 | TSPAN9 | chr12 | 3384815 | 3384835 |
pancreas | RPL27A | chr11 | 8707801 | 8707821 | TPH1 | chr11 | 18043985 | 18044005 |
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 RPL27A 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 |
CR936817 | MAN2C1 | 1 | 4827 | 15 | 75650091 | 75655518 | RPL27A | 4821 | 5455 | 11 | 8705338 | 8707393 | |
BF828517 | RPL27A | 85 | 115 | 11 | 8706408 | 8706438 | RPL27A | 108 | 213 | 11 | 8707262 | 8707367 |
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=4) | (# total SNVs=1) |
(# 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 |
chr11:8705620-8705620 | p.F45F | 1 |
chr11:8706299-8706299 | p.H60Y | 1 |
chr11:8706403-8706403 | p.K94N | 1 |
chr11:8706416-8706416 | p.P99S | 1 |
chr11:8707314-8707314 | p.K136N | 1 |
chr11:8707323-8707323 | p.S139R | 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 |   |   |   |   |   |   | 1 | 1 |   |   |   |   | 1 | 1 |   | 3 |
# mutation |   |   |   | 1 |   |   |   |   |   |   | 1 | 1 |   |   |   |   | 1 | 1 |   | 3 |
nonsynonymous SNV |   |   |   | 1 |   |   |   |   |   |   |   | 1 |   |   |   |   | 1 | 1 |   | 3 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   | 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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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 |
chr11:8705620 | p.A143G | 1 |
chr11:8706299 | p.F45F | 1 |
chr11:8706403 | p.H60Y | 1 |
chr11:8706410 | p.K94N | 1 |
chr11:8706416 | p.A97S | 1 |
chr11:8707314 | p.P99S | 1 |
chr11:8707323 | p.K136N | 1 |
chr11:8707334 | p.S139R | 1 |
Other DBs for Point Mutations |
Copy Number for RPL27A 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 RPL27A |
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 |
EIF3F,RPL11,RPL13,RPL14,RPL18,RPL24,RPL27A, RPL31,RPL32,RPL36,RPL37,RPL37A,RPLP2,RPS10, RPS11,RPS13,RPS18,RPS19,RPS2,RPS8,RPS9 | NME2,PFDN5,RPL10,RPL11,RPL12,RPL13,RPL18, RPL24,RPL27A,RPL36,RPL38,RPL7A,RPL8,RPLP1, RPS11,RPS14,RPS24,RPS3,RPS8,SNRPD2,SNRPF |
AKIP1,LCN15,RPL14,RPL24,RPL27A,RPL29,RPL32, RPL35A,RPL7A,RPS11,RPS13,RPS14,RPS15A,RPS18, RPS25,RPS3,RPS9,RPSA,RPSAP58,TMEM9B,TSSC4 | TMEM261,DPY30,EEF1B2,HSCB,LSM2,RPL24,RPL27A, RPL35,RPL35A,RPL41,RPS10,RPS11,RPS13,RPS14, RPS18,RPS3A,RPS5,RPS6,RPS7,RPS8,SNRPD2 |
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 RPL27A |
There's no related Drug. |
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Cross referenced IDs for RPL27A |
* 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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