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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RPL29 |
Basic gene info. | Gene symbol | RPL29 |
Gene name | ribosomal protein L29 | |
Synonyms | HIP|HUMRPL29|L29|RPL29P10|RPL29_3_370 | |
Cytomap | UCSC genome browser: 3p21.3-p21.2 | |
Genomic location | chr3 :52027643-52029958 | |
Type of gene | protein-coding | |
RefGenes | NM_000992.2, | |
Ensembl id | ENSG00000162244 | |
Description | 60S ribosomal protein L29HP/HS-interacting proteincell surface heparin-binding protein HIPheparin/heparan sulfate-binding proteinheparin/heparan sulfate-interacting proteinribosomal protein YL43 homologue | |
Modification date | 20141207 | |
dbXrefs | MIM : 601832 | |
HGNC : HGNC | ||
Ensembl : ENSG00000162244 | ||
HPRD : 03495 | ||
Vega : OTTHUMG00000155262 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RPL29 | |
BioGPS: 6159 | ||
Gene Expression Atlas: ENSG00000162244 | ||
The Human Protein Atlas: ENSG00000162244 | ||
Pathway | NCI Pathway Interaction Database: RPL29 | |
KEGG: RPL29 | ||
REACTOME: RPL29 | ||
ConsensusPathDB | ||
Pathway Commons: RPL29 | ||
Metabolism | MetaCyc: RPL29 | |
HUMANCyc: RPL29 | ||
Regulation | Ensembl's Regulation: ENSG00000162244 | |
miRBase: chr3 :52,027,643-52,029,958 | ||
TargetScan: NM_000992 | ||
cisRED: ENSG00000162244 | ||
Context | iHOP: RPL29 | |
cancer metabolism search in PubMed: RPL29 | ||
UCL Cancer Institute: RPL29 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RPL29(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: RPL29 |
Familial Cancer Database: RPL29 |
* 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/ |
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REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: RPL29 |
MedGen: RPL29 (Human Medical Genetics with Condition) | |
ClinVar: RPL29 | |
Phenotype | MGI: RPL29 (International Mouse Phenotyping Consortium) |
PhenomicDB: RPL29 |
Mutations for RPL29 |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPL29 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 |
AW860778 | CD74 | 14 | 385 | 5 | 149784690 | 149786889 | RPL29 | 374 | 535 | 3 | 52029055 | 52029930 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=7) | (# total SNVs=2) |
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(# total SNVs=1) | (# total SNVs=1) |
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* 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 |
chr3:52029073-52029073 | p.Y29* | 2 |
chr3:52027966-52027966 | p.L93L | 1 |
chr3:52027968-52027968 | p.L93F | 1 |
chr3:52028031-52028031 | p.I72F | 1 |
chr3:52028040-52028040 | p.A69T | 1 |
chr3:52028047-52028047 | p.S66S | 1 |
chr3:52027797-52027797 | p.R150G | 1 |
chr3:52027815-52027815 | p.P144S | 1 |
chr3:52029107-52029107 | p.R18K | 1 |
chr3:52027853-52027854 | p.K130_D131insAK | 1 |
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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 |   | 1 |   |   | 1 |   | 1 | 2 |   | 3 |
# mutation |   |   |   |   |   |   |   |   |   | 1 |   | 1 |   |   | 1 |   | 1 | 2 |   | 3 |
nonsynonymous SNV |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   | 1 |   | 1 |   |   | 2 |
synonymous SNV |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   | 2 |   | 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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* 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 |
chr3:52028040 | p.R111S | 1 |
chr3:52028047 | p.R95R | 1 |
chr3:52029074 | p.L93L | 1 |
chr3:52029107 | p.K73K | 1 |
chr3:52029445 | p.A69T | 1 |
chr3:52027797 | p.S66S | 1 |
chr3:52027815 | p.Y29C | 1 |
chr3:52027914 | p.R18K | 1 |
chr3:52027960 | p.N11N | 1 |
chr3:52027966 | p.R150G | 1 |
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* 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. |
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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 RPL29 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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RPL11,RPL12,RPL14,RPL15,RPL18,RPL24,RPL29, RPL32,RPL34,RPL35,RPL36,RPL37,RPL37A,RPL7A, RPLP2,RPS11,RPS14,RPS2,RPS4X,RPS8,RPS9 | PHB2,RPL10,RPL13,RPL13A,RPL14,RPL18,RPL18A, RPL19,RPL29,RPL32,RPL35,RPL36,RPL37,RPL37A, RPL7A,RPS14,RPS16,RPS2,RPS5,RPS6,RPS8 |
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RPL10A,RPL12,RPL14,RPL15,RPL24,RPL29,RPL32, RPL35,RPL35A,RPL37A,RPL7A,RPS13,RPS14,RPS15, RPS18,RPS23,RPS3,RPS8,RPS9,RPSA,RPSAP58 | ATP5G2,PHB2,RPL10,RPL10A,RPL13A,RPL14,RPL18, RPL18A,RPL19,RPL29,RPL32,RPL35,RPL7A,RPL8, RPLP0,RPLP1,RPS11,RPS14,RPS3,RPS5,RPS8 |
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* 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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Pharmacological Information for RPL29 |
There's no related Drug. |
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Cross referenced IDs for RPL29 |
* 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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