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 RPS7
Basic gene info.Gene symbolRPS7
Gene nameribosomal protein S7
SynonymsDBA8|S7
CytomapUCSC genome browser: 2p25
Genomic locationchr2 :3622852-3628509
Type of geneprotein-coding
RefGenesNM_001011.3,
Ensembl idENSG00000171863
Description40S ribosomal protein S7
Modification date20141219
dbXrefs MIM : 603658
HGNC : HGNC
Ensembl : ENSG00000171863
HPRD : 04712
Vega : OTTHUMG00000090305
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS7
BioGPS: 6201
Gene Expression Atlas: ENSG00000171863
The Human Protein Atlas: ENSG00000171863
PathwayNCI Pathway Interaction Database: RPS7
KEGG: RPS7
REACTOME: RPS7
ConsensusPathDB
Pathway Commons: RPS7
MetabolismMetaCyc: RPS7
HUMANCyc: RPS7
RegulationEnsembl's Regulation: ENSG00000171863
miRBase: chr2 :3,622,852-3,628,509
TargetScan: NM_001011
cisRED: ENSG00000171863
ContextiHOP: RPS7
cancer metabolism search in PubMed: RPS7
UCL Cancer Institute: RPS7
Assigned class in ccmGDBC

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Phenotypic Information for RPS7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS7
Familial Cancer Database: RPS7
* 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: RPS7
MedGen: RPS7 (Human Medical Genetics with Condition)
ClinVar: RPS7
PhenotypeMGI: RPS7 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS7

Mutations for RPS7
* 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 RPS7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP272543ATP6V0D11310166748751467515062RPS7308370236234143623476
U16258RPS71256236231893624177TONSL25418048145661993145668562

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=9)
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
chr2:3627755-3627755p.E138K2
chr2:3627805-3627805p.I154I2
chr2:3623237-3623237p.G13D1
chr2:3623448-3623448p.Q39H1
chr2:3627776-3627776p.R145C1
chr2:3623453-3623453p.R41K1
chr2:3627792-3627792p.G150D1
chr2:3623475-3623475p.A48A1
chr2:3627799-3627799p.R152R1
chr2:3624082-3624082p.I51I1

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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
# sample2  1       2    42 4
# mutation2  1       2    42 3
nonsynonymous SNV1  1            4  3
synonymous SNV1          2     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
chr2:3627755p.E138K2
chr2:3627805p.I154M2
chr2:3623448p.R41K1
chr2:3628430p.P65P1
chr2:3623453p.V93A1
chr2:3628456p.F135F1
chr2:3624124p.R145C1
chr2:3624207p.G150D1
chr2:3627748p.R152R1
chr2:3627776p.G175S1

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 RPS7 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 RPS7

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,RPL24,RPL27A,RPL31,RPL32,RPL35A,RPL37,
RPL37A,RPL5,RPL6,RPLP2,RPS10,RPS18,RPS19,
RPS27A,RPS6,RPS7,RPS8,SF3B14,SNRPA,UQCRH
RPL10,RPL12,RPL14,RPL22,RPL24,RPL32,RPL35A,
RPL37,RPL41,RPL4,RPL5,RPL6,RPLP0,RPS12,
RPS23,RPS24,RPS3A,RPS4X,RPS6,RPS7,RPS8

COA5,DPY30,EEF1B2,RPL10A,RPL24,RPL27,RPL31,
RPL32,RPL35,RPL36,RPL37A,RPL5,RPS10,RPS14,
RPS15A,RPS18,RPS21,RPS3,RPS6,RPS7,RPS8
C12orf29,KANSL2,COMMD10,DPY30,EEF1B2,HSCB,MED28,
PRDX3,RPL24,RPL35,RPL5,RPS14,RPS18,RPS3A,
RPS6,RPS7,RPS8,RSL24D1,SNRPD2,TMEM14B,ZFAND1
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 RPS7


There's no related Drug.
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Cross referenced IDs for RPS7
* 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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