Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for RPL12
Basic gene info.Gene symbolRPL12
Gene nameribosomal protein L12
SynonymsL12
CytomapUCSC genome browser: 9q34
Genomic locationchr9 :130209952-130213711
Type of geneprotein-coding
RefGenesNM_000976.3,
Ensembl idENSG00000197958
Description60S ribosomal protein L12
Modification date20141207
dbXrefs MIM : 180475
HGNC : HGNC
Ensembl : ENSG00000197958
HPRD : 01603
Vega : OTTHUMG00000020704
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL12
BioGPS: 6136
Gene Expression Atlas: ENSG00000197958
The Human Protein Atlas: ENSG00000197958
PathwayNCI Pathway Interaction Database: RPL12
KEGG: RPL12
REACTOME: RPL12
ConsensusPathDB
Pathway Commons: RPL12
MetabolismMetaCyc: RPL12
HUMANCyc: RPL12
RegulationEnsembl's Regulation: ENSG00000197958
miRBase: chr9 :130,209,952-130,213,711
TargetScan: NM_000976
cisRED: ENSG00000197958
ContextiHOP: RPL12
cancer metabolism search in PubMed: RPL12
UCL Cancer Institute: RPL12
Assigned class in ccmGDBC

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Phenotypic Information for RPL12(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL12
Familial Cancer Database: RPL12
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: RPL12
MedGen: RPL12 (Human Medical Genetics with Condition)
ClinVar: RPL12
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPL12 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF089907IKZF36208173792130937921511RPL122002829130209966130210198
AA036700SON1161213492646334926623RPL121562979130210625130211621
AW277039RPL129799130213603130213673RPL12763629130211563130213594

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=7)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr9:130210640-130210640p.R119G3
chr9:130211911-130211911p.T63S2
chr9:130211898-130211898p.R67R1
chr9:130211929-130211929p.R57K1
chr9:130210156-130210156p.A164A1
chr9:130211949-130211949p.T50T1
chr9:130210190-130210190p.D153V1
chr9:130211976-130211976p.V42fs*151
chr9:130210242-130210242p.A136T1
chr9:130213582-130213582p.F5F1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  1     1 1     112
# mutation1  1     1 1     112
nonsynonymous SNV           1      1 
synonymous SNV1  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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr9:130210620p.R117R1
chr9:130210644p.G102V1
chr9:130210690p.R67R1
chr9:130211898p.T50T1
chr9:130211949p.F5F1
chr9:130213582p.P3P1
chr9:130213588p.P3S1
chr9:130213590p.L125L1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

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
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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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

: Open all cross reference information



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