|
mutLBSgeneDB |
| |
| |
| |
| |
| |
| |
|
| Gene summary for PML |
 Gene summary |
| Basic gene Info. | Gene symbol | PML |
| Gene name | promyelocytic leukemia | |
| Synonyms | MYL|PP8675|RNF71|TRIM19 | |
| Cytomap | UCSC genome browser: 15q22 | |
| Type of gene | protein-coding | |
| RefGenes | NM_002675.3, NM_033238.2,NM_033239.2,NM_033240.2,NM_033244.3, NM_033246.2,NM_033247.2,NM_033249.2,NM_033250.2, | |
| Description | RING finger protein 71probable transcription factor PMLpromyelocytic leukemia proteinpromyelocytic leukemia, inducer ofprotein PMLtripartite motif protein TRIM19tripartite motif-containing protein 19 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 102578 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000140464 | ||
| HPRD : 00023 | ||
| Vega : OTTHUMG00000137607 | ||
| Protein | UniProt: P29590 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PML | |
| BioGPS: 5371 | ||
| Pathway | NCI Pathway Interaction Database: PML | |
| KEGG: PML | ||
| REACTOME: PML | ||
| Pathway Commons: PML | ||
| Context | iHOP: PML | |
| ligand binding site mutation search in PubMed: PML | ||
| UCL Cancer Institute: PML | ||
| Assigned class in mutLBSgeneDB | A: This gene has a literature evidence and it belongs to targetable_mutLBSgenes. | |
| References showing study about ligand binding site mutation for PML. | 1. "Zhou DC, Kim SH, Ding W, Schultz C, Warrell RP Jr, Gallagher RE. Frequent mutations in the ligand-binding domain of PML-RARalpha after multiple relapses of acute promyelocytic leukemia: analysis for functional relationship to response to all-trans retinoic acid and histone deacetylase inhibitors in vitro and in vivo. Blood. 2002 Feb 15;99(4):1356-63." 11830487 | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0001666 | response to hypoxia | 16915281 | GO:0006461 | protein complex assembly | 12915590 | GO:0006605 | protein targeting | 11080164 | GO:0006915 | apoptotic process | 9583681 | GO:0007050 | cell cycle arrest | 12773567 | GO:0008630 | intrinsic apoptotic signaling pathway in response to DNA damage | 12402044 | GO:0030308 | negative regulation of cell growth | 7935403 | GO:0030578 | PML body organization | 10779416 | GO:0031065 | positive regulation of histone deacetylation | 11259576 | GO:0032938 | negative regulation of translation in response to oxidative stress | 16915281 | GO:0034097 | response to cytokine | 9412458 | GO:0043161 | proteasome-mediated ubiquitin-dependent protein catabolic process | 22406621 | GO:0045087 | innate immune response | 18248090 | GO:0045892 | negative regulation of transcription, DNA-templated | 11259576 | GO:0045930 | negative regulation of mitotic cell cycle | 9395203 | GO:0050821 | protein stabilization | 12773567 | GO:0051457 | maintenance of protein location in nucleus | 17332504 | GO:0060058 | positive regulation of apoptotic process involved in mammary gland involution | 11080164 | GO:0090398 | cellular senescence | 22002537 | GO:1902187 | negative regulation of viral release from host cell | 18248090 |
| Top |
| Ligand binding site mutations for PML |
| Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.)  : non-synonymous mutation on LBS, Circle size denotes number of samples. |
 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | C143 | E142Q | BLCA | 1 | C88 | P89T | COAD | 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. |
| Top |
| Protein structure related information for PML |
| 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 |
 |
| 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 | C88 | P89T | -0.74353532 | C143 | E142Q | -0.47808004 |
| (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 PML from PDB |
| Top |
| Differential gene expression and gene-gene network for PML |
| 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) |
| Top |
| Top |
| Phenotype information for PML |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0023487 | Leukemia, Promyelocytic, Acute | 402 | AlteredExpression, Biomarker, GeneticVariation |
| umls:C0017636 | Glioblastoma | 3 | Biomarker |
| umls:C0029401 | Osteitis Deformans | 1 | Biomarker, GeneticVariation |
| umls:C0023904 | Liver Neoplasms, Experimental | 1 | Therapeutic |
| umls:C0085183 | Neoplasms, Second Primary | 1 | Biomarker |
| umls:C0036341 | Schizophrenia | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
| Top |
| Pharmacological information for PML |
| 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. |
 |
| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
 |
| Ligands binding to mutated ligand binding site of PML go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 2mvw | A | C143 | ZN | ZINC(2+) | 2mvw | B | C143 | ZN | ZINC(2+) | 2mwx | A | C88 |
| Top |
| Conservation information for LBS of PML |
| Multiple alignments for P29590 in multiple species |
| LBS | AA sequence | # species | Species |
 |
Copyright © 2016-Present - The University of Texas Health Science Center at Houston |