JOSD2 Data Analysis

HGNC Gene Name
Josephin domain containing 2
HGNC Gene Symbol
JOSD2
Identifiers
hgnc:28853 NCBIGene:126119 uniprot:Q8TAC2
Orthologs
mgi:1913374 rgd:1307305
INDRA Statements
deubiquitinations all statements
Pathway Commons
Search for JOSD2
Number of Papers
8 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 JOSD2using 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 JOSD2 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
PITX2 affects JOSD2
2 |
PITX2 decreases the amount of JOSD2. 2 / 2
2 |

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available
Niclosamide affects JOSD2
2 |
Niclosamide increases the amount of JOSD2. 2 / 2
2 |

ctd
No evidence text available

ctd
No evidence text available
ELK1 affects JOSD2
2 |
ELK1 decreases the amount of JOSD2. 2 / 2
2 |

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available
6-propyl-2-thiouracil decreases the amount of JOSD2. 2 / 2
2 |

ctd
No evidence text available

ctd
No evidence text available
| 1 1
| 1

reach
JOSD2 deficiency displays cytostatic effects and reduces glycolysis in a broad spectrum of tumor cells of distinct origin and its expression correlates with poor prognosis in non small cell lung cancer.
| 1

eidos
JOSD2 deficiency displays cytostatic effects and reduces glycolysis in a broad spectrum of tumor cells of distinct origin and its expression correlates with poor prognosis in non-small cell lung cancer .
2,3,7,8-tetrachlorodibenzodioxine increases the amount of JOSD2.
1 |
1 |

ctd
No evidence text available
2,3,7,8-tetrachlorodibenzodioxine decreases the amount of JOSD2.
1 |
1 |

ctd
No evidence text available
17alpha-ethynylestradiol increases the amount of JOSD2.
1 |
17alpha-ethynylestradiol increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
17alpha-ethynylestradiol decreases the amount of JOSD2.
1 |
17alpha-ethynylestradiol decreases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Zinc atom affects JOSD2
1 |
Zinc atom increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
1 |
Valproic acid increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Topotecan affects JOSD2
1 |
Topotecan decreases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Tetrachloromethane increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
1 |
Sodium arsenite increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Oxaliplatin affects JOSD2
1 |
Oxaliplatin decreases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Nefazodone affects JOSD2
1 |
Nefazodone increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Methyl methanesulfonate increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Glafenine affects JOSD2
1 |
Glafenine increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Flutamide affects JOSD2
1 |
Flutamide increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Decabromodiphenyl ether decreases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
1 |
Cyclosporin A increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Coumarin affects JOSD2
1 |
Coumarin increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
1 |
Cobalt dichloride decreases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Cadmium dichloride increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Atrazine affects JOSD2
1 |
Atrazine increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
1 |
Aluminium atom decreases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
Acetamide affects JOSD2
1 |
Acetamide increases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
TFAP2C affects JOSD2
1 |
TFAP2C decreases the amount of JOSD2. 1 / 1
1 |

biopax:msigdb
No evidence text available
TFAP2A affects JOSD2
1 |
TFAP2A decreases the amount of JOSD2. 1 / 1
1 |

biopax:msigdb
No evidence text available
SP3 affects JOSD2
1 |
SP3 decreases the amount of JOSD2. 1 / 1
1 |

biopax:msigdb
No evidence text available

ctd
No evidence text available
RFX1 affects JOSD2
1 |
RFX1 decreases the amount of JOSD2. 1 / 1
1 |

biopax:msigdb
No evidence text available
PAX4 affects JOSD2
1 |
PAX4 decreases the amount of JOSD2. 1 / 1
1 |

biopax:msigdb
No evidence text available
PAX3 affects JOSD2
1 |
PAX3 decreases the amount of JOSD2. 1 / 1
1 |

biopax:msigdb
No evidence text available
MEF2A affects JOSD2
1 |
MEF2A decreases the amount of JOSD2. 1 / 1
1 |

biopax:msigdb
No evidence text available
JOSD2 affects cell death
| 1
| 1

reach
Furthermore, in contrast to the control siRNA treated cells, siRNA depletion of JOSD2 caused selective cell death in high-PHGDH-expressing cells, but not in low expressing cell lines.
ICG 001 affects JOSD2
1 |
ICG 001 decreases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
GCM1 affects JOSD2
1 |
GCM1 decreases the amount of JOSD2. 1 / 1
1 |

biopax:msigdb
No evidence text available
GATA1 affects JOSD2
1 |
GATA1 decreases the amount of JOSD2. 1 / 1
1 |

biopax:msigdb
No evidence text available
1 |
C646 compound decreases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
AR affects JOSD2
1 |
AR decreases the amount of JOSD2. 1 / 1
1 |

biopax:msigdb
No evidence text available
1 |
(+)-JQ1 compound decreases the amount of JOSD2. 1 / 1
1 |

ctd
No evidence text available
1 |

ctd
No evidence text available