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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RPL12 |
Basic gene info. | Gene symbol | RPL12 |
Gene name | ribosomal protein L12 | |
Synonyms | L12 | |
Cytomap | UCSC genome browser: 9q34 | |
Genomic location | chr9 :130209952-130213711 | |
Type of gene | protein-coding | |
RefGenes | NM_000976.3, | |
Ensembl id | ENSG00000197958 | |
Description | 60S ribosomal protein L12 | |
Modification date | 20141207 | |
dbXrefs | MIM : 180475 | |
HGNC : HGNC | ||
Ensembl : ENSG00000197958 | ||
HPRD : 01603 | ||
Vega : OTTHUMG00000020704 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RPL12 | |
BioGPS: 6136 | ||
Gene Expression Atlas: ENSG00000197958 | ||
The Human Protein Atlas: ENSG00000197958 | ||
Pathway | NCI Pathway Interaction Database: RPL12 | |
KEGG: RPL12 | ||
REACTOME: RPL12 | ||
ConsensusPathDB | ||
Pathway Commons: RPL12 | ||
Metabolism | MetaCyc: RPL12 | |
HUMANCyc: RPL12 | ||
Regulation | Ensembl's Regulation: ENSG00000197958 | |
miRBase: chr9 :130,209,952-130,213,711 | ||
TargetScan: NM_000976 | ||
cisRED: ENSG00000197958 | ||
Context | iHOP: RPL12 | |
cancer metabolism search in PubMed: RPL12 | ||
UCL Cancer Institute: RPL12 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RPL12(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: RPL12 |
Familial Cancer Database: RPL12 |
* 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: RPL12 |
MedGen: RPL12 (Human Medical Genetics with Condition) | |
ClinVar: RPL12 | |
Phenotype | MGI: RPL12 (International Mouse Phenotyping Consortium) |
PhenomicDB: RPL12 |
Mutations for RPL12 |
* 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 RPL12 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 |
BF089907 | IKZF3 | 6 | 208 | 17 | 37921309 | 37921511 | RPL12 | 200 | 282 | 9 | 130209966 | 130210198 | |
AA036700 | SON | 1 | 161 | 21 | 34926463 | 34926623 | RPL12 | 156 | 297 | 9 | 130210625 | 130211621 | |
AW277039 | RPL12 | 9 | 79 | 9 | 130213603 | 130213673 | RPL12 | 76 | 362 | 9 | 130211563 | 130213594 |
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=7) | (# total SNVs=5) |
(# total SNVs=1) | (# 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 |
chr9:130210640-130210640 | p.R119G | 3 |
chr9:130211911-130211911 | p.T63S | 2 |
chr9:130210156-130210156 | p.A164A | 1 |
chr9:130211949-130211949 | p.T50T | 1 |
chr9:130210190-130210190 | p.D153V | 1 |
chr9:130211976-130211976 | p.V42fs*15 | 1 |
chr9:130210242-130210242 | p.A136T | 1 |
chr9:130213582-130213582 | p.F5F | 1 |
chr9:130210253-130210253 | p.I132S | 1 |
chr9:130213588-130213588 | p.P3P | 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 | 1 | 2 |
# mutation | 1 |   |   | 1 |   |   |   |   |   | 1 |   | 1 |   |   |   |   |   | 1 | 1 | 2 |
nonsynonymous SNV |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | 1 |   |
synonymous SNV | 1 |   |   | 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 |
chr9:130210620 | p.L125L | 1 |
chr9:130210644 | p.R117R | 1 |
chr9:130210690 | p.G102V | 1 |
chr9:130211898 | p.R67R | 1 |
chr9:130211949 | p.T50T | 1 |
chr9:130213582 | p.F5F | 1 |
chr9:130213588 | p.P3P | 1 |
chr9:130213590 | p.P3S | 1 |
Other DBs for Point Mutations |
Copy Number for RPL12 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 RPL12 |
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 |
RPL11,RPL12,RPL14,RPL18,RPL24,RPL29,RPL31, RPL32,RPL34,RPL35,RPL36,RPL37,RPL37A,RPL6, RPL7A,RPS11,RPS14,RPS18,RPS2,RPS4X,RPS8 | EEF1G,EIF3D,FBL,GNB2L1,RPL10,RPL10A,RPL12, RPL14,RPL32,RPL5,RPL6,RPL7A,RPLP0,RPS18, RPS2,RPS3,RPS4X,RPS6,RPS7,RPS8,RPSAP58 |
GNB2L1,RPL10A,RPL12,RPL29,RPL31,RPL32,RPL34, RPL35,RPL35A,RPL3,RPL36,RPL37A,RPL5,RPL7A, RPLP0,RPS23,RPS25,RPS2,RPS6,RPS8,RPS9 | EEF1A1,EEF1A1P9,FAU,RPL10,RPL10A,RPL12,RPL15, RPL19,RPL30,RPL32,RPL35A,RPL3,RPL5,RPL6, RPL7A,RPL8,RPS11,RPS12,RPS13,RPS23,RPS25 |
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 RPL12 |
There's no related Drug. |
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Cross referenced IDs for RPL12 |
* 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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