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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RPL7 |
Basic gene info. | Gene symbol | RPL7 |
Gene name | ribosomal protein L7 | |
Synonyms | L7|humL7-1 | |
Cytomap | UCSC genome browser: 8q21.11 | |
Genomic location | chr8 :74202873-74205869 | |
Type of gene | protein-coding | |
RefGenes | NM_000971.3, | |
Ensembl id | ENSG00000147604 | |
Description | 60S ribosomal protein L7 | |
Modification date | 20141207 | |
dbXrefs | MIM : 604166 | |
HGNC : HGNC | ||
Ensembl : ENSG00000147604 | ||
HPRD : 05004 | ||
Vega : OTTHUMG00000134312 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RPL7 | |
BioGPS: 6129 | ||
Gene Expression Atlas: ENSG00000147604 | ||
The Human Protein Atlas: ENSG00000147604 | ||
Pathway | NCI Pathway Interaction Database: RPL7 | |
KEGG: RPL7 | ||
REACTOME: RPL7 | ||
ConsensusPathDB | ||
Pathway Commons: RPL7 | ||
Metabolism | MetaCyc: RPL7 | |
HUMANCyc: RPL7 | ||
Regulation | Ensembl's Regulation: ENSG00000147604 | |
miRBase: chr8 :74,202,873-74,205,869 | ||
TargetScan: NM_000971 | ||
cisRED: ENSG00000147604 | ||
Context | iHOP: RPL7 | |
cancer metabolism search in PubMed: RPL7 | ||
UCL Cancer Institute: RPL7 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RPL7(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: RPL7 |
Familial Cancer Database: RPL7 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: RPL7 |
MedGen: RPL7 (Human Medical Genetics with Condition) | |
ClinVar: RPL7 | |
Phenotype | MGI: RPL7 (International Mouse Phenotyping Consortium) |
PhenomicDB: RPL7 |
Mutations for RPL7 |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPL7 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BG394529 | SLC4A2 | 2 | 671 | 7 | 150756751 | 150761984 | RPL7 | 662 | 737 | 8 | 74202904 | 74203318 | |
DA454229 | RPL7 | 1 | 410 | 8 | 74205458 | 74205867 | AP1G2 | 407 | 591 | 14 | 24030899 | 24031083 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
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) |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=12) | (# total SNVs=6) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr8:74204479-74204479 | p.I95I | 3 |
chr8:74203895-74203895 | p.Y144H | 1 |
chr8:74204972-74204972 | p.F25F | 1 |
chr8:74204012-74204012 | p.W142R | 1 |
chr8:74204982-74204982 | p.R22Q | 1 |
chr8:74204024-74204024 | p.P138S | 1 |
chr8:74205017-74205017 | p.E10E | 1 |
chr8:74205020-74205022 | p.K9delK | 1 |
chr8:74203428-74203428 | p.R200C | 1 |
chr8:74204485-74204485 | p.I93I | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 3 |   | 6 |   |   |   |   | 1 |   |   | 2 | 1 |   |   |   | 1 | 1 |   | 2 |
# mutation | 1 | 3 |   | 5 |   |   |   |   | 1 |   |   | 2 | 1 |   |   |   | 1 | 1 |   | 2 |
nonsynonymous SNV | 1 | 1 |   | 4 |   |   |   |   | 1 |   |   | 1 | 1 |   |   |   | 1 | 1 |   | 1 |
synonymous SNV |   | 2 |   | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr8:74204982 | p.R22Q | 2 |
chr8:74204485 | p.R43Q | 1 |
chr8:74204500 | p.K40Q | 1 |
chr8:74204636 | p.A38A | 1 |
chr8:74204929 | p.F25F | 1 |
chr8:74203428 | p.E10E | 1 |
chr8:74204933 | p.E5K | 1 |
chr8:74203795 | p.R200C | 1 |
chr8:74204972 | p.V4G | 1 |
chr8:74203803 | p.R177Q | 1 |
Other DBs for Point Mutations |
Copy Number for RPL7 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 RPL7 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for RPL7 |
There's no related Drug. |
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Cross referenced IDs for RPL7 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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