Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 RPL36A
Basic gene info.Gene symbolRPL36A
Gene nameribosomal protein L36a
SynonymsL36A|L44L|MIG6|RPL44
CytomapUCSC genome browser: Xq22.1
Genomic locationchrX :100645877-100651142
Type of geneprotein-coding
RefGenesNM_001199972.1,
NM_021029.5,
Ensembl idENSG00000269315
Description60S ribosomal protein L36a60S ribosomal protein L44L44-like ribosomal proteincell growth-inhibiting gene 15 proteincell migration-inducing gene 6 proteindJ164F3.3 (ribosomal protein L44)
Modification date20141207
dbXrefs MIM : 300902
HGNC : HGNC
Ensembl : ENSG00000241343
HPRD : 06709
Vega : OTTHUMG00000022027
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL36A
BioGPS: 6173
Gene Expression Atlas: ENSG00000269315
The Human Protein Atlas: ENSG00000269315
PathwayNCI Pathway Interaction Database: RPL36A
KEGG: RPL36A
REACTOME: RPL36A
ConsensusPathDB
Pathway Commons: RPL36A
MetabolismMetaCyc: RPL36A
HUMANCyc: RPL36A
RegulationEnsembl's Regulation: ENSG00000269315
miRBase: chrX :100,645,877-100,651,142
TargetScan: NM_001199972
cisRED: ENSG00000269315
ContextiHOP: RPL36A
cancer metabolism search in PubMed: RPL36A
UCL Cancer Institute: RPL36A
Assigned class in ccmGDBC

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Phenotypic Information for RPL36A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL36A
Familial Cancer Database: RPL36A
* 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: RPL36A
MedGen: RPL36A (Human Medical Genetics with Condition)
ClinVar: RPL36A
PhenotypeMGI: RPL36A (International Mouse Phenotyping Consortium)
PhenomicDB: RPL36A

Mutations for RPL36A
* 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 RPL36A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE540117ZNF19512571133812623381519RPL36A252624X100645962100650446

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=5)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=2)
There's no deleted 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
chr23:100646036-100646036p.?2
chr23:100650445-100650445p.K100K2
chr23:100646742-100646742p.?2
chr23:100646748-100646748p.R39W1
chr23:100646780-100646780p.G49G1
chr23:100646803-100646803p.R57Q1
chr23:100646034-100646034p.M1I1
chr23:100646812-100646812p.?1
chr23:100650321-100650321p.?1
chr23:100646445-100646445p.?1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                  1 
# mutation                  1 
nonsynonymous SNV                    
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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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
chrX:100650727p.I140I1

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 RPL36A 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 RPL36A

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

CDCA3,EIF5AL1,FAM136A,LYAR,MRPL9,NOP2,NPM3,
PFDN2,PUS1,RPL35A,RPL36A,RPS24,RPS2,RPS7,
SF3B14,SNHG1,SNHG3,SNRPA,TIMM8A,UCK2,UQCRH
AHCY,ZFAS1,FAM83A,GINS2,GNB2L1,IMPDH2,DANCR,
NPM1,PRPS2,RPL10A,RPL12,RPL36A,RPS18,RPS24,
RPS4X,S100A14,SMPDL3B,NELFCD,TPRXL,TSPAN1,WNT4

HIST1H4K,LCE2B,LOC100132247,LOC613037,FTX,OR6N2,OR8B3,
POTEE,PPIAL4G,PRAMEF17,PRAMEF3,RPL13AP20,RPL13AP6,RPL21,
RPL36A,RPL39,RPS26P11,RPSAP9,SNORA38,SNORD16,SNORD35B,
SNORD88C,TBC1
ATAD5,BLM,BRIP1,RMI2,ZGRF1,CHAF1B,CHEK1,
CSTF3,DTL,EHF,FAM111B,GPX2,JAK2,KNTC1,
LOC100129066,MCM7,RPL36A,SHCBP1,TIFA,TMEM173,TYMS
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 RPL36A


There's no related Drug.
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Cross referenced IDs for RPL36A
* 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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