USP54 Data Analysis

HGNC Gene Name
ubiquitin specific peptidase 54
HGNC Gene Symbol
USP54
Identifiers
hgnc:23513 NCBIGene:159195 uniprot:Q70EL1
Orthologs
mgi:1926037 rgd:1303206
INDRA Statements
deubiquitinations all statements
Pathway Commons
Search for USP54
Number of Papers
9 retrieved on 2022-05-22

DepMap Analysis

The Dependency Map (DepMap) is a genome-wide pooled CRISPR-Cas9 knockout proliferation screen conducted in more than 700 cancer cell lines spanning many different tumor lineages. Each cell line in the DepMap contains a unique barcode, and each gene knockout is assigned a “dependency score” on a per cell-line basis which quantifies the rate of CRISPR-Cas9 guide drop. It has been found that proteins with similar DepMap scores across cell lines, a phenomenon known as co-dependent genes, have closely related biological functions. This can include activity in the same or parallel pathways or membership in the same protein complex or the same pathway.

We identified the strongest seven co-dependent genes (“Symbol”) for DUBs and ran GO enrichment analysis. We used Biogrid, IntAct, and Pathway Commons PPIDs, and the NURSA protein-protein interaction databases (PPIDs) to determine whether co-dependent genes interact with one another. The “Evidence” column contains the PPIDs in which the interaction appears as well as whether there is support for the association by an INDRA statement. As another approach to identify potential interactors, we looked at proteomics data from the Broad Institute's Cancer Cell Line Encyclopedia (CCLE) for proteins whose expression across ~375 cell lines strongly correlated with the abundance of each DUB; it has previously been observed that proteins in the same complex are frequently significantly co-expressed. The correlations and associated p-values in the CCLE proteomics dataset are provided. And, we determined whether co-dependent genes yield similar transcriptomic signatures in the Broad Institute's Connectivity Map (CMap). A CMap score greater than 90 is considered significantly similar.

DepMap Correlations

Symbol Name DepMap Correlation Evidence CCLE Correlation CCLE Z-score CCLE p-value (adj) CCLE Significant CMAP Score CMAP Type

Dependency GO Term Enrichment

Gene set enrichment analysis was done on the genes correlated with USP54using the terms from Gene Ontology and gene sets derived from the Gene Ontology Annotations database via MSigDB.

Using the biological processes and other Gene Ontology terms from well characterized DUBs as a positive control, several gene set enrichment analyses were considered. Threshold-less methods like GSEA had relatively poor results. Over-representation analysis with a threshold of of the top 7 highest absolute value Dependency Map correlations yielded the best results and is reported below.

GO Identifier GO Name GO Type p-value p-value (adj.) q-value

Literature Mining

INDRA was used to automatically assemble known mechanisms related to USP54 from literature and knowledge bases. The first section shows only DUB activity and the second shows all other results.

Deubiquitinase Activity

Other Statements

psp cbn pc bel_lc signor biogrid lincs_drug tas hprd trrust ctd vhn pe drugbank omnipath conib crog dgi | rlimsp isi tees geneways eidos trips medscan sparser reach
AR affects USP54
4 |
AR decreases the amount of USP54. 4 / 4
4 |

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available
4 |
Benzo[a]pyrene increases the amount of USP54.
2 |
Benzo[a]pyrene increases the amount of USP54. 2 / 2
2 |

ctd
No evidence text available

ctd
No evidence text available
Benzo[a]pyrene decreases the amount of USP54.
2 |
Benzo[a]pyrene decreases the amount of USP54. 2 / 2
2 |

ctd
No evidence text available

ctd
No evidence text available
NR3C1 affects USP54
3 |
NR3C1 decreases the amount of USP54. 3 / 3
3 |

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available
Bisphenol A affects USP54
3 |
Bisphenol A increases the amount of USP54.
2 |
Bisphenol A increases the amount of USP54. 2 / 2
2 |

ctd
No evidence text available

ctd
No evidence text available
Bisphenol A decreases the amount of USP54.
1 |
Bisphenol A decreases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
TCF3 affects USP54
2 |
TCF3 decreases the amount of USP54. 2 / 2
2 |

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available
PGR affects USP54
2 |
PGR decreases the amount of USP54. 2 / 2
2 |

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available
MYOD1 affects USP54
2 |
MYOD1 decreases the amount of USP54. 2 / 2
2 |

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available

reach
Similarly, USP54 downregulation decreased the invasiveness of HCT116 cells.
| 1

reach
USP54 promotes cancer invasion in chemically induced colorectal carcinomas.
2,3,7,8-tetrachlorodibenzodioxine increases the amount of USP54.
1 |
1 |

ctd
No evidence text available
2,3,7,8-tetrachlorodibenzodioxine decreases the amount of USP54.
1 |
1 |

ctd
No evidence text available
1 |
Valproic acid increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Triphenyl phosphate increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Tetrachloromethane increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Nickel atom affects USP54
1 |
Nickel atom decreases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Monosodium L-glutamate decreases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Methyl methanesulfonate increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
1 |
Methamphetamine increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
1 |
Hsa-miR-215-5p decreases the amount of USP54. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-192-5p decreases the amount of USP54. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-1303 decreases the amount of USP54. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-let-7b-5p decreases the amount of USP54. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Fluoranthene increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Ethanol affects USP54
1 |
Ethanol increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Doxorubicin affects USP54
1 |
Doxorubicin decreases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Dicrotophos affects USP54
1 |
Dicrotophos increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
1 |
Dexamethasone increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Decamethrin affects USP54
1 |
Decamethrin increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Coumestrol affects USP54
1 |
Coumestrol decreases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Clobetasol affects USP54
1 |
Clobetasol increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
1 |
Aflatoxin B1 increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Abrine affects USP54
1 |
Abrine increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
USP54 affects WDR37
| 1
USP54 inhibits WDR37. 1 / 1
| 1

reach
PIF Increased the expression of : (USP54, BRD2, ARRB2) and decreased the expression of (WDR37, CUL1, SIAHA, HIC2.
USP54 affects CUL1
| 1
USP54 inhibits CUL1. 1 / 1
| 1

reach
PIF Increased the expression of : (USP54, BRD2, ARRB2) and decreased the expression of (WDR37, CUL1, SIAHA, HIC2.
USP54 affects CRC
| 1
USP54 activates CRC. 1 / 1
| 1

reach
Accordingly, silencing of USP54 in colorectal cancer (CRC) cells led to a significant decrease in cell proliferation, colony formation capacity, invasiveness, and tumorigenicity in an in vivo xenograft model, indicating that USP54 could promote CRC, potentially by controlling stem cell properties in intestinal cells.
UBP1 affects USP54
1 |
UBP1 decreases the amount of USP54. 1 / 1
1 |

biopax:msigdb
No evidence text available
1 |
Trans Fatty Acids decreases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
TNF affects USP54
| 1
TNF activates USP54. 1 / 1
| 1

reach
Nonetheless, a minimum of two siRNA molecules led to increased levels of nuclear NF-kappaB in A549 cells depleted of A20, USP7, USP49, USP54, or FBXO36 and treated with TNF for 120min.
TFAP4 affects USP54
1 |
TFAP4 decreases the amount of USP54. 1 / 1
1 |

biopax:msigdb
No evidence text available
Soot affects USP54
1 |
Soot increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
REPIN1 affects USP54
1 |
REPIN1 decreases the amount of USP54. 1 / 1
1 |

biopax:msigdb
No evidence text available
PITX2 affects USP54
1 |
PITX2 decreases the amount of USP54. 1 / 1
1 |

biopax:msigdb
No evidence text available
MAZ affects USP54
1 |
MAZ decreases the amount of USP54. 1 / 1
1 |

biopax:msigdb
No evidence text available
LEF1 affects USP54
1 |
LEF1 decreases the amount of USP54. 1 / 1
1 |

biopax:msigdb
No evidence text available
GSK-J4 affects USP54
1 |
GSK-J4 decreases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
FOXO4 affects USP54
1 |
FOXO4 decreases the amount of USP54. 1 / 1
1 |

biopax:msigdb
No evidence text available
1 |
Dietary Fats increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
Antirheumatic Agents increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
6-propyl-2-thiouracil decreases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
17alpha-ethynylestradiol increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
1-methylanthracene increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
1,3-dinitrobenzene increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
4,4'-diaminodiphenylmethane increases the amount of USP54. 1 / 1
1 |

ctd
No evidence text available
1 |

ctd
No evidence text available