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mutLBSgeneDB |
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| Gene summary for PDLIM1 |
 Gene summary |
| Basic gene Info. | Gene symbol | PDLIM1 |
| Gene name | PDZ and LIM domain 1 | |
| Synonyms | CLIM1|CLP-36|CLP36|HEL-S-112|hCLIM1 | |
| Cytomap | UCSC genome browser: 10q23.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_020992.3, | |
| Description | LIM domain protein CLP-36PDZ and LIM domain protein 1carboxyl terminal LIM domain protein 1elfinepididymis secretory protein Li 112 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 605900 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000107438 | ||
| HPRD : 09326 | ||
| Vega : OTTHUMG00000018810 | ||
| Protein | UniProt: O00151 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PDLIM1 | |
| BioGPS: 9124 | ||
| Pathway | NCI Pathway Interaction Database: PDLIM1 | |
| KEGG: PDLIM1 | ||
| REACTOME: PDLIM1 | ||
| Pathway Commons: PDLIM1 | ||
| Context | iHOP: PDLIM1 | |
| ligand binding site mutation search in PubMed: PDLIM1 | ||
| UCL Cancer Institute: PDLIM1 | ||
| 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 PDLIM1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | C286 | C286R | COAD | 1 | H310 | R312L | LUAD | 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 PDLIM1 |
| 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 | C286 | C286R | -0.55795769 | H310 | R312L | -0.53784871 |
| (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 PDLIM1 from PDB |
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| Differential gene expression and gene-gene network for PDLIM1 |
| 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 PDLIM1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for PDLIM1 |
| 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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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PDLIM1 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 PDLIM1 |
| Multiple alignments for O00151 in multiple species |
| LBS | AA sequence | # species | Species | C260 | QKLPMCDKCGT | 2 | Homo sapiens, Bos taurus | C260 | QKLPICDKCGT | 2 | Mus musculus, Rattus norvegicus | C263 | PMCDKCGTGIV | 2 | Homo sapiens, Bos taurus | C263 | PICDKCGTGIV | 2 | Mus musculus, Rattus norvegicus | C283 | HRHPECYVCTD | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | C286 | PECYVCTDCGT | 2 | Homo sapiens, Bos taurus | C286 | PECYVCTDCGI | 2 | Mus musculus, Rattus norvegicus | C289 | YVCTDCGTNLK | 2 | Homo sapiens, Bos taurus | C289 | YVCTDCGINLK | 2 | Mus musculus, Rattus norvegicus | C307 | EDQIYCEKHAR | 3 | Homo sapiens, Mus musculus, Bos taurus | C307 | GDQIYCEKHAR | 1 | Rattus norvegicus | H280 | RDHHRHPECYV | 2 | Mus musculus, Rattus norvegicus | H280 | RDRHRHPECYV | 1 | Homo sapiens | H280 | RERHRHPECYV | 1 | Bos taurus | H310 | IYCEKHARERV | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus |
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