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 RPL28
Basic gene info.Gene symbolRPL28
Gene nameribosomal protein L28
SynonymsL28
CytomapUCSC genome browser: 19q13.4
Genomic locationchr19 :55897299-55903451
Type of geneprotein-coding
RefGenesNM_000991.4,
NM_001136134.1,NM_001136135.1,NM_001136136.1,NM_001136137.1,
Ensembl idENSG00000108107
Description60S ribosomal protein L28
Modification date20141207
dbXrefs MIM : 603638
HGNC : HGNC
Ensembl : ENSG00000108107
HPRD : 04702
Vega : OTTHUMG00000171991
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL28
BioGPS: 6158
Gene Expression Atlas: ENSG00000108107
The Human Protein Atlas: ENSG00000108107
PathwayNCI Pathway Interaction Database: RPL28
KEGG: RPL28
REACTOME: RPL28
ConsensusPathDB
Pathway Commons: RPL28
MetabolismMetaCyc: RPL28
HUMANCyc: RPL28
RegulationEnsembl's Regulation: ENSG00000108107
miRBase: chr19 :55,897,299-55,903,451
TargetScan: NM_000991
cisRED: ENSG00000108107
ContextiHOP: RPL28
cancer metabolism search in PubMed: RPL28
UCL Cancer Institute: RPL28
Assigned class in ccmGDBC

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Phenotypic Information for RPL28(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL28
Familial Cancer Database: RPL28
* 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: RPL28
MedGen: RPL28 (Human Medical Genetics with Condition)
ClinVar: RPL28
PhenotypeMGI: RPL28 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL28

Mutations for RPL28
* 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 RPL28 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA524376RPL281366195589730055899416GLB136651033311406333114206
BE388585RPL28457195589772255897775LASP153366173707628037076593
BE387849RPL28356195589772255897775LASP152366173707628037076593
BG748632RPL281601195589731455899746ZNF804B59061178848205088482071
AW498880RPL281160195589937555899730GAPDH1613911266440026645955
BQ653766BCYRN11643X7051408570517282RPL28636690195589968655899740
BC004230RPL2844532195589731155899744TPI152917531269767026979993
AA776201RPL281106195589961155899717EPB41L1106374203477321834776411
BQ648662CBWD221562114223330114223370RPL2839504195589771755899743
BC009885RPL2844532195589731155899744TPI152917531269767026979993
BQ645838CBWD221562114223330114223370RPL2839504195589771755899743
BU543829ANGPTL4407671984363478439255RPL28768885195589731255897809
BG473709DDX11729021576049215767242RPL28272739195589730055899708
BQ646046CBWD222572114223330114223370RPL2840505195589771755899743
AI907286RPL2812158195589773655898013RPL28150247195589802755899360
DB253394RPL2833360195589771655899410C22orf23357559223834010338340305
BQ649823CBWD222572114223330114223370RPL2840505195589771755899743

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=12)
Stat. for Synonymous SNVs
(# total SNVs=2)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr19:55898050-55898050p.K65M1
chr19:55899405-55899405p.D105N1
chr19:55899311-55899311p.P73P1
chr19:55899632-55899632p.A116T1
chr19:55899328-55899328p.R79L1
chr19:55899675-55899675p.R130Q1
chr19:55899329-55899329p.R79R1
chr19:55897738-55897738p.L5V1
chr19:55899332-55899332p.T80T1
chr19:55897765-55897765p.S14P1

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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
# sample1  3  2 2  31  111 4
# mutation1  3  2 2  31  111 4
nonsynonymous SNV1  3  1 2  21  1 1 3
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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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
chr19:55898050p.R79R,RPL281
chr19:55902965p.T80T,RPL281
chr19:55899311p.R87S,RPL281
chr19:55899328p.A88A,RPL281
chr19:55899329p.S91R,RPL281
chr19:55897738p.R103H,RPL281
chr19:55899332p.L5V,RPL281
chr19:55897765p.D105N,RPL281
chr19:55899351p.S14P,RPL281
chr19:55897779p.R130Q1

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 RPL28 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 RPL28

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

ATP5D,FAU,HSPBP1,NDUFA3,RPL13,RPL13A,RPL13AP20,
RPL18,RPL28,RPL29,RPL35,RPL36,RPL37A,RPLP2,
RPS11,RPS15,RPS19,RPS5,RPS9,ZNF524,ZNF579
DNAJC4,ETHE1,FAU,MRPS2,RPL13,RPL13A,RPL18,
RPL18A,RPL19,RPL28,RPL29,RPL35,RPL36,RPP21,
RPS15,RPS16,RPS19,RPS21,RPS9,SLC27A5,ZNF581

GLTSCR2,RPL13,RPL13A,RPL18,RPL28,RPL36,RPL38,
RPLP0,RPLP2,RPS11,RPS15,RPS16,RPS19,RPS2,
RPS3,RPS5,RPS9,SNRPD2,UBA52,ZNF524,ZNF581
ATPAF2,EEF1G,EIF3D,EIF3F,GNB2L1,MACROD1,MAPKAPK3,
NOB1,QTRT1,RPL13,RPL18,RPL28,RPL36,RPL37,
RPLP2,RPS15,RPS19,RPS2,SLC25A6,UBA52,ZNF524
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 RPL28


There's no related Drug.
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Cross referenced IDs for RPL28
* 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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