An interaction is inferred when a bait-enzyme fusion protein selectively modifies a vicinal protein with a diffusible reactive product, followed by affinity capture of the modified protein and identification by mass spectrometric methods.

Publication

Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression.

Malaymar Pinar D, Goeoes H, Tan Z, Kumpula EP, Chowdhury I, Wang Z, Zhang Q, Salokas K, Keskitalo S, Wei GH, Kumbasar A, Varjosalo M

The Nuclear Factor I (NFI) family of transcription factors (TFs) plays key roles in cellular differentiation, proliferation, and homeostasis. As such, NFI family members engage in a large number of interactions with other proteins and chromatin. However, despite their well-established significance, the NFIs' interactomes, their dynamics, and their functions have not been comprehensively examined. Here, we employed complementary omics-level techniques, ... [more]

Mol Cell Proteomics Jan. 01, 2025; 24(1);100890 [Pubmed: 39617063]

Throughput

High Throughput

Additional Notes

BioID
Filtered HCIs from 16h Biotinylated MAC3N tagged NFIX expressing Flp-In T-REx 293 cell lines. Interactions with Saint assigned Bayesian FDR of over 0.01 were discarded, but interactors that passed this filtering in any dataset were rescued. Interactors with an average spectral count less than 3 were also discarded. Preys detected in 20 percent or more of CRAPome experiments were discarded unless they were rescued by having a spectral count in the experiments over three times higher than in CRAPome
Filtered HCIs from 3h Biotinylated MAC3N tagged NFIX expressing Flp-In T-REx 293 cell lines. Interactions with Saint assigned Bayesian FDR of over 0.01 were discarded, but interactors that passed this filtering in any dataset were rescued. Interactors with an average spectral count less than 3 were also discarded. Preys detected in 20 percent or more of CRAPome experiments were discarded unless they were rescued by having a spectral count in the experiments over three times higher than in CRAPome

Related interactions

Interaction	Experimental Evidence Code	Dataset	Throughput	Score	Curated By	Notes
NFIX SKI	Phenotypic Enhancement Phenotypic Enhancement A genetic interaction is inferred when mutation or overexpression of one gene results in enhancement of any phenotype (other than lethality/growth defect) associated with mutation or over expression of another gene.	Tarapore P (1997)	Low	-	BioGRID	-
SKI NFIX	Reconstituted Complex Reconstituted Complex An interaction is inferred between proteins in vitro. This can include proteins in recombinant form or proteins isolated directly from cells with recombinant or purified bait. For example, GST pull-down assays where a GST-tagged protein is first isolated and then used to fish interactors from cell lysates are considered reconstituted complexes (e.g. PUBMED: 14657240, Fig. 4A or PUBMED: 14761940, Fig. 5). This can also include gel-shifts, surface plasmon resonance, isothermal titration calorimetry (ITC) and bio-layer interferometry (BLI) experiments. The bait-hit directionality may not be clear for 2 interacting proteins. In these cases the directionality is up to the discretion of the curator.	Tarapore P (1997)	Low	-	BioGRID	-

Curated By

BioGRID

Interaction Summary

NFIX

Gene Ontology Biological Process

Gene Ontology Molecular Function

RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity [TAS]sequence-specific DNA binding transcription factor activity [TAS]

Gene Ontology Cellular Component

SKI