ArticleMolecular & cellular proteomics : MCP2014
Controlling for gene expression changes in transcription factor protein networks.
Article in Molecular & cellular proteomics : MCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed, 25 citations in OpenAlex.
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- Distinct Regions within SAP25 Recruit O-Linked Glycosylation, DNA Demethylation, and Ubiquitin Ligase and Hydrolase Activities to the Sin3/HDAC Complex.Journal of proteome research · 2024Article
- Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression.NAR genomics and bioinformatics · 2023Article
- Integrative Modeling of a Sin3/HDAC Complex Sub-structure.Cell reports · 2020Article
- Quantifying Tissue-Specific Overexpression of FOXO in Drosophila via mRNA Fluorescence In Situ Hybridization Using Branched DNA Probe Technology.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Gene regulatory network construction identified NFYA as a diffuse subtype-specific prognostic factor in gastric cancer.International journal of oncology · 2018Article
- Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly.Scientific reports · 2018Article
- A Structured Workflow for Mapping Human Sin3 Histone Deacetylase Complex Interactions Using Halo-MudPIT Affinity-Purification Mass Spectrometry.Molecular & cellular proteomics : MCP · 2018Article
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- Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer.Oncotarget · 2017Article
- Identification of Novel Nuclear Factor of Activated T Cell (NFAT)-associated Proteins in T Cells.The Journal of biological chemistry · 2016Article
- TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions.Molecular & cellular proteomics : MCP · 2016Article
- Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components.Molecular & cellular proteomics : MCP · 2016Article
- Assembly of the Elongin A Ubiquitin Ligase Is Regulated by Genotoxic and Other Stresses.The Journal of biological chemistry · 2015Article
- Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C.Nature communications · 2015Article
- Proteins interacting with cloning scars: a source of false positive protein-protein interactions.Scientific reports · 2015Article
- Conserved abundance and topological features in chromatin-remodeling protein interaction networks.EMBO reports · 2015Article
- Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The development of affinity purification technologies combined with mass spectrometric analysis of purified protein mixtures has been used both to identify new protein-protein interactions and to define the subunit composition of protein complexes. Transcription factor protein interactions, however, have not been systematically analyzed using these approaches. Here, we investigated whether ectopic expression of an affinity tagged transcription factor as bait in affinity purification mass spectrometry experiments perturbs gene expression in cells, resulting in the false positive identification of bait-associated proteins when typical experimental controls are used. Using quantitative proteomics and RNA sequencing, we determined that the increase in the abundance of a set of proteins caused by overexpression of the transcription factor RelA is not sufficient for these proteins to then co-purify non-specifically and be misidentified as bait-associated proteins. Therefore, typical controls should be sufficient, and a number of different baits can be compared with a common set of controls. This is of practical interest when identifying bait interactors from a large number of different baits. As expected, we found several known RelA interactors enriched in our RelA purifications (NFκB1, NFκB2, Rel, RelB, IκBα, IκBβ, and IκBε). We also found several proteins not previously described in association with RelA, including the small mitochondrial chaperone Tim13. Using a variety of biochemical approaches, we further investigated the nature of the association between Tim13 and NFκB family transcription factors. This work therefore provides a conceptual and experimental framework for analyzing transcription factor protein interactions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.