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 RPL22
Basic gene info.Gene symbolRPL22
Gene nameribosomal protein L22
SynonymsEAP|HBP15|HBP15/L22|L22
CytomapUCSC genome browser: 1p36.31
Genomic locationchr1 :6245079-6259679
Type of geneprotein-coding
RefGenesNM_000983.3,
Ensembl idENSG00000116251
Description60S ribosomal protein L22EBER-associated proteinEpstein-Barr virus small RNA-associated proteinEpstein-Barr-encoded RNA-associated proteinheparin-binding protein 15heparin-binding protein HBp15
Modification date20141207
dbXrefs MIM : 180474
HGNC : HGNC
Ensembl : ENSG00000116251
HPRD : 01602
Vega : OTTHUMG00000000953
ProteinUniProt: P35268
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL22
BioGPS: 6146
Gene Expression Atlas: ENSG00000116251
The Human Protein Atlas: ENSG00000116251
PathwayNCI Pathway Interaction Database: RPL22
KEGG: RPL22
REACTOME: RPL22
ConsensusPathDB
Pathway Commons: RPL22
MetabolismMetaCyc: RPL22
HUMANCyc: RPL22
RegulationEnsembl's Regulation: ENSG00000116251
miRBase: chr1 :6,245,079-6,259,679
TargetScan: NM_000983
cisRED: ENSG00000116251
ContextiHOP: RPL22
cancer metabolism search in PubMed: RPL22
UCL Cancer Institute: RPL22
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPL22(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL22
Familial Cancer Database: RPL22
* 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 UCEC 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
7Therapeutic 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 180474; gene.
Orphanet
DiseaseKEGG Disease: RPL22
MedGen: RPL22 (Human Medical Genetics with Condition)
ClinVar: RPL22
PhenotypeMGI: RPL22 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL22

Mutations for RPL22
* 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 RPL22 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU858788MAP3K23992128062363128062459RPL2293464162460946246465
CR738829RPL221314162453846245697DLC130170381294088212941285
BF846664RPL227224162458236246042PCSK621652515101870984101871293

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=15)
Stat. for Synonymous SNVs
(# total SNVs=1)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=2)

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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
chr1:6257785-6257785p.K15fs*56
chr1:6246877-6246877p.?2
chr1:6259633-6259633p.M1L2
chr1:6257784-6257785p.K16fs*92
chr1:6246808-6246808p.A104D2
chr1:6257826-6257826p.?1
chr1:6246818-6246818p.R101C1
chr1:6253009-6253009p.E75*1
chr1:6259621-6259621p.?1
chr1:6246830-6246830p.R97C1

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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
# sample 1 3  1 1  1 1  1  4
# mutation 1 3  1 1  1 1  1  4
nonsynonymous SNV   2  1 1  1 1  1  4
synonymous SNV 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
chr1:6246830p.R101H1
chr1:6246831p.R101C1
chr1:6246851p.R97C1
chr1:6246853p.L96L1
chr1:6246855p.Y90H1
chr1:6246862p.K89T1
chr1:6253065p.K88N1
chr1:6253091p.L86P1
chr1:6253107p.L56P1
chr1:6246817p.I47M1

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 RPL22 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 RPL22

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

NACA,RPL10A,RPL11,RPL12,RPL17,RPL22,RPL31,
RPL34,RPL3,RPL4,RPL5,RPL6,RPL7A,RPLP0,
RPS13,RPS18,RPS23,RPS25,RPS4X,RPS6,RPS8
BTF3,CCT4,EEF1A1,NPM1,RPL15,RPL22,RPL23A,
RPL30,RPL32,RPL34,RPL35A,RPL5,RPL6,RPS15A,
RPS23,RPS24,RPS27A,RPS3A,RPS4X,RPS6,RPS7

CAMTA1,HNRNPA1,LRRC47,MRTO4,NACA,PARK7,RMND1,
RPL11,RPL12,RPL22,RPL34,RPL3,RPL37,RPL37A,
RPL5,RPL6,RPS24,RPS25,RPS2,RPS27A,UBIAD1
CDKAL1,EIF2S3,EIF3H,EIF3L,EIF4B,FBL,HNRNPA1,
HNRNPA1L2,IMPDH2,LARS,LTA4H,MATR3,NACA,PAIP2B,
RPL11,RPL22,RPL23A,RPL37,RPL7,SMU1,ZNF830
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 RPL22


There's no related Drug.
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Cross referenced IDs for RPL22
* 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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