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mutLBSgeneDB |
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| Gene summary for RNASE4 |
 Gene summary |
| Basic gene Info. | Gene symbol | RNASE4 |
| Gene name | ribonuclease, RNase A family, 4 | |
| Synonyms | RAB1|RNS4 | |
| Cytomap | UCSC genome browser: 14q11 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001282192.1, NM_001282193.1,NM_002937.4,NM_194431.2,NM_194430.1, | |
| Description | RNase 4ribonuclease 4ribonuclease A B1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 601030 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000258818 | ||
| HPRD : 03018 | ||
| Vega : OTTHUMG00000029575 | ||
| Protein | UniProt: P34096 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RNASE4 | |
| BioGPS: 6038 | ||
| Pathway | NCI Pathway Interaction Database: RNASE4 | |
| KEGG: RNASE4 | ||
| REACTOME: RNASE4 | ||
| Pathway Commons: RNASE4 | ||
| Context | iHOP: RNASE4 | |
| ligand binding site mutation search in PubMed: RNASE4 | ||
| UCL Cancer Institute: RNASE4 | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID |
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| Ligand binding site mutations for RNASE4 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | R129 | R129T | BLCA | 1 | R129 | V131I | COAD | 1 | R129 | R130C | GBM | 1 | G19 | G19E | LUAD | 1 | F145 | G147D | SKCM | 1 | Q39 | R38Q | STAD | 1 |
| cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, 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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| Protein structure related information for RNASE4 |
| Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
 : nsSNV at non-LBS : nsSNV at LBS |
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| nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
| LBS | AAchange of nsSNV | Relative stability change | R129 | R130C | -1.0776191 | R129 | R129T | -1.0670892 | F145 | G147D | -0.92200932 | Q39 | R38Q | -0.82638079 | G19 | G19E | -0.63493091 | R129 | V131I | -0.62698526 |
| (MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
| Structure image for RNASE4 from PDB |
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| Differential gene expression and gene-gene network for RNASE4 |
| Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
| Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
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| Phenotype information for RNASE4 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0023893 | Liver Cirrhosis, Experimental | 1 | Biomarker |
| umls:C0033578 | Prostatic Neoplasms | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for RNASE4 |
| Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Experimental | DB03448 | 2'-Deoxyuridine 3'-Monophosphate | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of RNASE4 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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| Conservation information for LBS of RNASE4 |
| Multiple alignments for P34096 in multiple species |
| LBS | AA sequence | # species | Species | D30 | PSYGQDGMYQR | 2 | Homo sapiens, Pan troglodytes | D30 | PSYGQDRMYQR | 1 | Rattus norvegicus | F145 | QVPVHFDG | 2 | Homo sapiens, Pan troglodytes | F145 | EVPVHFDR | 1 | Rattus norvegicus | F70 | YHCKRFNTFIH | 2 | Homo sapiens, Pan troglodytes | F70 | TQCKRFNTFIH | 1 | Rattus norvegicus | G19 | LLTLLGLGLVQ | 3 | Homo sapiens, Pan troglodytes, Rattus norvegicus | H144 | PQVPVHFDG | 2 | Homo sapiens, Pan troglodytes | H144 | PEVPVHFDR | 1 | Rattus norvegicus | H40 | RFLRQHVHPEE | 2 | Homo sapiens, Pan troglodytes | H40 | RFLRQHVDPEG | 1 | Rattus norvegicus | K68 | TLYHCKRFNTF | 2 | Homo sapiens, Pan troglodytes | K68 | TSTQCKRFNTF | 1 | Rattus norvegicus | N71 | HCKRFNTFIHE | 2 | Homo sapiens, Pan troglodytes | N71 | QCKRFNTFIHE | 1 | Rattus norvegicus | Q39 | QRFLRQHVHPE | 2 | Homo sapiens, Pan troglodytes | Q39 | QRFLRQHVDPE | 1 | Rattus norvegicus | R129 | AIASTRRVVIA | 1 | Homo sapiens | R129 | AMASTRRVVIA | 1 | Pan troglodytes | R129 | ARASTRRVVIA | 1 | Rattus norvegicus | R35 | DGMYQRFLRQH | 2 | Homo sapiens, Pan troglodytes | R35 | DRMYQRFLRQH | 1 | Rattus norvegicus | T72 | CKRFNTFIHED | 3 | Homo sapiens, Pan troglodytes, Rattus norvegicus |
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