MINDY1 Data Analysis

HGNC Gene Name
MINDY lysine 48 deubiquitinase 1
HGNC Gene Symbol
MINDY1
Identifiers
hgnc:25648 NCBIGene:55793 uniprot:Q8N5J2
Orthologs
mgi:1922257 rgd:1559660
INDRA Statements
deubiquitinations all statements
Pathway Commons
Search for MINDY1
Number of Papers
7 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
CIART circadian associated repressor of transcription 0.385
CTSK cathepsin K 0.349
H2AC21 H2A clustered histone 21 0.328 0.01 -0.04 9.25e-01
CD48 CD48 molecule 0.318
TNFAIP8L2 TNF alpha induced protein 8 like 2 0.313
GABPB2 GA binding protein transcription factor subunit beta 2 0.312 INDRA (1) 0.19 0.97 3.04e-02
THBS3 thrombospondin 3 0.31 -0.06 -0.41 6.21e-01

Dependency GO Term Enrichment

Gene set enrichment analysis was done on the genes correlated with MINDY1using 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 MINDY1 from literature and knowledge bases. The first section shows only DUB activity and the second shows all other results.

Deubiquitinase Activity

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
MINDY1 leads to the deubiquitination of endoplasmic reticulum. 1 / 1
| 1

reach
Specifically, MINDY1 associated with the N-terminal of ERα via its catalytic domain, thus inhibiting K48-specific poly-ubiquitination process on ERα protein.

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
MYB affects MINDY1
4 |
MYB decreases the amount of MINDY1. 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 |
Pirinixic acid increases the amount of MINDY1.
2 |
Pirinixic acid increases the amount of MINDY1. 2 / 2
2 |

ctd
No evidence text available

ctd
No evidence text available
Pirinixic acid decreases the amount of MINDY1.
1 |
Pirinixic acid decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
Pirinixic acid activates MINDY1.
1 |

ctd
No evidence text available
LEF1 affects MINDY1
2 |
LEF1 decreases the amount of MINDY1. 2 / 2
2 |

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available
FOXO4 affects MINDY1
2 |
FOXO4 decreases the amount of MINDY1. 2 / 2
2 |

biopax:msigdb
No evidence text available

biopax:msigdb
No evidence text available
2 |
Bisphenol A increases the amount of MINDY1.
1 |
Bisphenol A increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
Bisphenol A decreases the amount of MINDY1.
1 |
Bisphenol A decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
Trimethyltin chloride increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
1 |
Sulforaphane decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
1 |
Nickel monoxide increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
1 |
Methotrexate increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
1 |
Leflunomide decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
Jinfukang affects MINDY1
1 |
Jinfukang increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
1 |
Hsa-miR-8062 decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-7151-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6832-5p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6807-5p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6778-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6747-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6727-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6513-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-6504-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-5096 decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-5095 decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-483-5p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4740-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4722-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4700-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4465 decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4433b-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4433a-3p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-4279 decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-411-5p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-3653-5p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-26b-5p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-26a-5p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-1976 decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-193b-5p decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-1303 decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
1 |
Hsa-miR-1297 decreases the amount of MINDY1. 1 / 1
1 |

biopax:mirtarbase
No evidence text available
Gossypol acetic acid decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
1 |
Formaldehyde increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
Flutamide affects MINDY1
1 |
Flutamide increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available

reach
Finally, overexpression of ERα could rescue the MINDY1 depletion-induced growth inhibition both in vitro and in vivo, suggesting that MINDY1 promotes breast carcinogenesis through increasing ERα stability.
Dimethyl-4-toluidine decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
Dibutyl phthalate increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
1 |
Cyclosporin A decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
Clofibrate affects MINDY1
1 |
Clofibrate decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
Cisplatin affects MINDY1
1 |
Cisplatin increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
1 |
Cadmium atom decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
Atrazine affects MINDY1
1 |
Atrazine increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
All-trans-retinoic acid increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
Tobacco Smoke Pollution increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
TFAP4 affects MINDY1
1 |
TFAP4 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
TCF4 affects MINDY1
1 |
TCF4 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
STAT6 affects MINDY1
1 |
STAT6 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
STAT5A affects MINDY1
1 |
STAT5A decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
STAT1 affects MINDY1
1 |
STAT1 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
RUNX1 affects MINDY1
1 |
RUNX1 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
REPIN1 affects MINDY1
1 |
REPIN1 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
Pentosan Sulfuric Polyester increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
PAX4 affects MINDY1
1 |
PAX4 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
MINDY1 increases the amount of endoplasmic reticulum. 1 / 1
| 1

reach
MINDY1 depletion significantly decreased the ERα protein level and ERα signaling activity in breast cancer cells.

reach
MINDY1 promotes breast cancer cell proliferation by stabilizing estrogen receptor α.

reach
In addition, MINDY1 depletion led to growth inhibition and cell cycle arrest of ERα-positive breast cancer cells.
MEIS1 affects MINDY1
1 |
MEIS1 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
HNF1A affects MINDY1
1 |
HNF1A decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
GABPB2 affects MINDY1
1 |
GABPB2 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
GABPA affects MINDY1
1 |
GABPA decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
FOXJ1 affects MINDY1
1 |
FOXJ1 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
ETV7 affects MINDY1
1 |
ETV7 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
ETV4 affects MINDY1
1 |
ETV4 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
ESR1 affects MINDY1
1 |
ESR1 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
ELK1 affects MINDY1
1 |
ELK1 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
CUX1 affects MINDY1
1 |
CUX1 decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
CEBPA affects MINDY1
1 |
CEBPA decreases the amount of MINDY1. 1 / 1
1 |

biopax:msigdb
No evidence text available
4-hydroxyphenyl retinamide increases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available

ctd
No evidence text available
2-monochloropropanediol decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
2-hydroxypropanoic acid decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available
1 |

ctd
No evidence text available
1 |
17beta-estradiol decreases the amount of MINDY1. 1 / 1
1 |

ctd
No evidence text available