MINDY2 Data Analysis

HGNC Gene Name
MINDY lysine 48 deubiquitinase 2
HGNC Gene Symbol
MINDY2
Identifiers
hgnc:26954 NCBIGene:54629 uniprot:Q8NBR6
Orthologs
mgi:2443086 rgd:1311456
INDRA Statements
deubiquitinations all statements
Pathway Commons
Search for MINDY2
Number of Papers
4 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
NBEAL1 neurobeachin like 1 0.28 -0.04 -0.28 7.36e-01
FOXD4 forkhead box D4 0.279
TSPYL5 TSPY like 5 0.278 -0.09 -0.61 2.11e-01
CNIH4 cornichon family AMPA receptor auxiliary protein 4 0.27 0.06 0.27 4.20e-01
KCNMB1 potassium calcium-activated channel subfamily M regulatory beta subunit 1 0.248
JAZF1 JAZF zinc finger 1 0.247
PRSS37 serine protease 37 0.242

Dependency GO Term Enrichment

Gene set enrichment analysis was done on the genes correlated with MINDY2using 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 MINDY2 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
3 |
Valproic acid increases the amount of MINDY2.
2 |
Valproic acid increases the amount of MINDY2. 2 / 2
2 |

ctd
No evidence text available

ctd
No evidence text available
Valproic acid decreases the amount of MINDY2.
1 |
Valproic acid decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
3 |
Pirinixic acid decreases the amount of MINDY2.
2 |
Pirinixic acid decreases the amount of MINDY2. 2 / 2
2 |

ctd
No evidence text available

ctd
No evidence text available
Pirinixic acid activates MINDY2.
1 |

ctd
No evidence text available
2 |
Carbon nanotube decreases the amount of MINDY2. 2 / 2
2 |

ctd
No evidence text available

ctd
No evidence text available
2 |
Bisphenol A increases the amount of MINDY2.
1 |
Bisphenol A increases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
Bisphenol A decreases the amount of MINDY2.
1 |
Bisphenol A decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Troglitazone decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
Succimer affects MINDY2
1 |
Succimer decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Sodium arsenite decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Sodium arsenate increases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Propiconazole decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Phenobarbital decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
Miconazole affects MINDY2
1 |
Miconazole decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
Methylmercury chloride decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Methamphetamine increases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
Magnetite nanoparticle decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Hydroperoxide decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Hsa-miR-769-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-7151-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-7-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6851-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6832-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6823-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6759-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6728-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6513-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6504-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-619-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6077 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-5580-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-5100 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-510-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-5096 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-5095 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-5089-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-494-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4802-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4781-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4755-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4670-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4524b-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4524a-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-450b-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4438 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4435 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4425 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4252 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-411-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-409-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-3942-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-375 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-335-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-3190-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-3185 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-3147 decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-197-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-192-5p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-1273g-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-124-3p decreases the amount of MINDY2. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
Flutamide affects MINDY2
1 |
Flutamide decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Doxorubicin decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
Diuron affects MINDY2
1 |
Diuron increases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
Clofibrate affects MINDY2
1 |
Clofibrate decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
Cisplatin affects MINDY2
1 |
Cisplatin decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Chlorpyrifos decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Chloroprene increases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
1 |
Aflatoxin B1 increases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
TLX2 affects MINDY2
1 |
TLX2 decreases the amount of MINDY2. 1 / 1
1 |

biopax:msigdb
No evidence text available
Soman affects MINDY2
1 |
Soman decreases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
SREBF1 affects MINDY2
1 |
SREBF1 decreases the amount of MINDY2. 1 / 1
1 |

biopax:msigdb
No evidence text available

ctd
No evidence text available
RUNX2 affects MINDY2
1 |
RUNX2 decreases the amount of MINDY2. 1 / 1
1 |

biopax:msigdb
No evidence text available
1 |
Plant Extracts increases the amount of MINDY2. 1 / 1
1 |

ctd
No evidence text available
NF1 affects MINDY2
1 |
NF1 decreases the amount of MINDY2. 1 / 1
1 |

biopax:msigdb
No evidence text available
MEF2A affects MINDY2
1 |
MEF2A decreases the amount of MINDY2. 1 / 1
1 |

biopax:msigdb
No evidence text available
ELK1 affects MINDY2
1 |
ELK1 decreases the amount of MINDY2. 1 / 1
1 |

biopax:msigdb
No evidence text available