Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 RPL7A
Basic gene info.Gene symbolRPL7A
Gene nameribosomal protein L7a
SynonymsL7A|SURF3|TRUP
CytomapUCSC genome browser: 9q34
Genomic locationchr9 :136215068-136218280
Type of geneprotein-coding
RefGenesNM_000972.2,
Ensembl idENSG00000260501
Description60S ribosomal protein L7aPLA-X polypeptidesurfeit 3surfeit locus protein 3thyroid hormone receptor uncoupling protein
Modification date20141207
dbXrefs MIM : 185640
HGNC : HGNC
Ensembl : ENSG00000148303
HPRD : 01712
Vega : OTTHUMG00000020864
ProteinUniProt: P62424
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL7A
BioGPS: 6130
Gene Expression Atlas: ENSG00000260501
The Human Protein Atlas: ENSG00000260501
PathwayNCI Pathway Interaction Database: RPL7A
KEGG: RPL7A
REACTOME: RPL7A
ConsensusPathDB
Pathway Commons: RPL7A
MetabolismMetaCyc: RPL7A
HUMANCyc: RPL7A
RegulationEnsembl's Regulation: ENSG00000260501
miRBase: chr9 :136,215,068-136,218,280
TargetScan: NM_000972
cisRED: ENSG00000260501
ContextiHOP: RPL7A
cancer metabolism search in PubMed: RPL7A
UCL Cancer Institute: RPL7A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for RPL7A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL7A
Familial Cancer Database: RPL7A
* 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 185640; gene.
Orphanet
DiseaseKEGG Disease: RPL7A
MedGen: RPL7A (Human Medical Genetics with Condition)
ClinVar: RPL7A
PhenotypeMGI: RPL7A (International Mouse Phenotyping Consortium)
PhenomicDB: RPL7A

Mutations for RPL7A
* 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 RPL7A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA868683RPL7A1689136217701136217768ST7-AS1685497116593398116759710
BU681467RPL7A175639136216808136218282CDH1562685166884606768847239
BC012174RPL7A148729136215776136218281RDX873170511110128554110167324
X06704RPL7A11549136215069136215897NTRK115415581156844362156851642

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample   1             
GAIN (# sample)   1             
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=12)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr9:136217156-136217156p.H159H2
chr9:136215778-136215778p.P2R2
chr9:136215864-136215864p.L31V2
chr9:136216484-136216484p.A68G1
chr9:136217531-136217531p.R192H1
chr9:136216489-136216489p.L70I1
chr9:136217870-136217870p.A214T1
chr9:136216554-136216554p.T91T1
chr9:136217921-136217921p.D231N1
chr9:136216773-136216773p.Q94R1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample  111   1  11   14 2
# mutation  111   1  11   14 2
nonsynonymous SNV  11    1  11   12 2
synonymous SNV    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])

Top
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
chr9:136216438p.R53S3
chr9:136217156p.H159H2
chr9:136217103p.D160N1
chr9:136217157p.F169L1
chr9:136217463p.K185N1
chr9:136217511p.A214T1
chr9:136217870p.L253L1
chr9:136218179p.E260E1
chr9:136218200p.A68G1
chr9:136216484p.Q94R1

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 RPL7A 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]

Top
Gene Expression for RPL7A

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

: Open all plots for all cancer types


Top
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

GNB2L1,NACA,RPL10A,RPL11,RPL12,RPL13A,RPL24,
RPL29,RPL31,RPL32,RPL35,RPL3,RPL37A,RPL6,
RPL7A,RPS11,RPS14,RPS18,RPS2,RPS4X,RPS8
EEF1G,FBL,GNB2L1,NOB1,RPL10,RPL12,RPL13,
RPL13A,RPL14,RPL18,RPL19,RPL29,RPL3,RPL36,
RPL7A,RPL8,RPS14,RPS18,RPS2,RPS3,RPS8

RPL10A,RPL12,RPL24,RPL29,RPL31,RPL32,RPL35,
RPL35A,RPL36,RPL37A,RPL7A,RPS10,RPS12,RPS14,
RPS18,RPS23,RPS25,RPS27A,RPS6,RPS8,RPS9
EEF1A1,EEF1A1P9,RPL10,RPL10A,RPL12,RPL14,RPL15,
RPL19,RPL29,RPL32,RPL3,RPL7A,RPL8,RPLP0,
RPLP1,RPS11,RPS12,RPS13,RPS3,RPS5,RPS8
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for RPL7A


There's no related Drug.
Top
Cross referenced IDs for RPL7A
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas