ArticleScientific reports2015
Proteins interacting with cloning scars: a source of false positive protein-protein interactions.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- HIT-MAP: A scalable approach to multimodal mapping of subcellular organization.Cell reports methods · 2026Article
- Unravelling the human taste receptor interactome: machine learning and molecular modelling insights into protein-protein interactions.NPJ science of food · 2025Article
- 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
- Studying Cellular Dynamics Using Proximity-Dependent Biotinylation: Somatic Cell Reprogramming.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- A standard for near-scarless plasmid construction using reusable DNA parts.Nature communications · 2019Article
- Topological scoring of protein interaction networks.Nature communications · 2019Article
- Purification and enzymatic assay of class I histone deacetylase enzymes.Methods in enzymology · 2019Article
- 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
- Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex.The FEBS journal · 2017Article
- TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions.Molecular & cellular proteomics : MCP · 2016Article
- Recent advances in large-scale protein interactome mapping.F1000Research · 2016Review
- WDR76 Co-Localizes with Heterochromatin Related Proteins and Rapidly Responds to DNA Damage.PloS one · 2016Article
- Quantitative affinity purification mass spectrometry: a versatile technology to study protein-protein interactions.Frontiers in genetics · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A common approach for exploring the interactome, the network of protein-protein interactions in cells, uses a commercially available ORF library to express affinity tagged bait proteins; these can be expressed in cells and endogenous cellular proteins that copurify with the bait can be identified as putative interacting proteins using mass spectrometry. Control experiments can be used to limit false-positive results, but in many cases, there are still a surprising number of prey proteins that appear to copurify specifically with the bait. Here, we have identified one source of false-positive interactions in such studies. We have found that a combination of: 1) the variable sequence of the C-terminus of the bait with 2) a C-terminal valine "cloning scar" present in a commercially available ORF library, can in some cases create a peptide motif that results in the aberrant co-purification of endogenous cellular proteins. Control experiments may not identify false positives resulting from such artificial motifs, as aberrant binding depends on sequences that vary from one bait to another. It is possible that such cryptic protein binding might occur in other systems using affinity tagged proteins; this study highlights the importance of conducting careful follow-up studies where novel protein-protein interactions are suspected.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.