Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps.

PLoS Computational Biology
Hailiang HuangJoel S Bader

Abstract

Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins. The fraction of interactions detected in independent screens can be very small, and an outstanding challenge is to determine the reason for the low overlap. Low overlap can arise from either a high false-discovery rate (interaction sets have low overlap because each set is contaminated by a large number of stochastic false-positive interactions) or a high false-negative rate (interaction sets have low overlap because each misses many true interactions). We extend capture-recapture theory to provide the first unified model for false-positive and false-negative rates for two-hybrid screens. Analysis of yeast, worm, and fly data indicates that 25% to 45% of the reported interactions are likely false positives. Membrane proteins have higher false-discovery rates on average, and signal transduction proteins have lower rates. The overall false-negative rate ranges from 75% for worm to 90% for fly, which arises from a roughly 50% false-negative rate due to statistical undersampling and a 55% to 85% false-negative rate due to proteins that appear to be systematically lost from the assays. Finally, statistical model selection co...Continue Reading

References

Apr 1, 1977·Theoretical Population Biology·J F Kingman
Jan 1, 1987·Journal of Mathematical Biology·F M Hoppe
Aug 30, 1985·Science·G D RoseM H Zehfus
Oct 1, 1974·Theoretical Population Biology·W J Ewens
Mar 1, 1972·Theoretical Population Biology·W J Ewens
Oct 15, 1984·Journal of Molecular Biology·D EisenbergR Wall
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Oct 16, 1999·Science·A L Barabasi, R Albert
Nov 26, 1999·Nature·E M MarcotteD Eisenberg
Feb 24, 2001·Nature·J C RainP Legrain
Apr 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·T ItoY Sakaki
May 3, 2001·Nature·H JeongZ N Oltvai
Apr 17, 2002·Physical Review Letters·Stefano MossaLuís A Nunes Amaral
Jul 16, 2002·Molecular & Cellular Proteomics : MCP·Charlotte M DeaneDavid Eisenberg
Mar 14, 2003·Nature·Eric PhizickyStanley Fields
Apr 19, 2003·Scientific American·Albert-László Barabási, Eric Bonabeau
Jul 11, 2003·Nucleic Acids Research·Andrei Grigoriev
Nov 8, 2003·Science·L GiotJ M Rothberg
Dec 4, 2003·Biochemical Society Transactions·A ThomasC Cannings
Dec 9, 2003·Nature Biotechnology·Michael Lappe, Liisa Holm
Dec 19, 2003·Nucleic Acids Research·Alex BatemanSean R Eddy
Dec 19, 2003·Nucleic Acids Research·Lukasz SalwinskiDavid Eisenberg
Jan 6, 2004·Science·Siming LiMarc Vidal
Jan 6, 2004·Nature Biotechnology·Joel S BaderJohn Chant
Feb 12, 2004·Bioinformatics·Ivan IossifovAndrey Rzhetsky
Mar 23, 2004·Bioinformatics·Michael A GilchristAndreas Wagner
Nov 30, 2004·Science·Insuk LeeEdward M Marcotte
Dec 17, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·J F Fontanari, L I Perlovsky
Feb 16, 2005·Genome Research·Etienne FormstecherLaurent Daviet
Mar 16, 2005·Proceedings of the National Academy of Sciences of the United States of America·Michael P H StumpfRobert M May
May 20, 2005·Neural Computation·Bruno M Jedynak, Sanjeev Khudanpur
Jul 9, 2005·Nature Biotechnology·Jing-Dong J HanMarc Vidal
Dec 31, 2005·Nucleic Acids Research·Chris StarkMike Tyers
Dec 31, 2005·Proceedings of the National Academy of Sciences of the United States of America·Eric J DeedsEugene I Shakhnovich
Jan 18, 2006·Science·Joel S Bader, John Chant
Jan 24, 2006·Nature·Anne-Claude GavinGiulio Superti-Furga

❮ Previous
Next ❯

Citations

Nov 16, 2013·Trends in Plant Science·Seung Yon Rhee, Marek Mutwil
Apr 3, 2008·Genome Research·Trey Ideker, Roded Sharan
Dec 9, 2008·Nature Methods·Kavitha VenkatesanMarc Vidal
Dec 19, 2008·Bioinformatics·Hailiang Huang, Joel S Bader
May 30, 2009·Bioinformatics·Chung-Shou LiaoBonnie Berger
Sep 5, 2009·PLoS Pathogens·Even FossumJürgen Haas
Jan 22, 2010·International Journal of Computational Biology and Drug Design·Xiaoyun Sun, Pengyu Hong
Mar 5, 2010·BMC Bioinformatics·Corban G RiveraJoel S Bader
Oct 3, 2012·PLoS Computational Biology·Anna C F LewisCharlotte M Deane
Sep 21, 2013·Nature Reviews. Genetics·Koyel MitraTrey Ideker
Jun 24, 2008·European Biophysics Journal : EBJ·Michael J Harris, Hyung-June Woo
Jan 1, 2013·Nucleic Acids Research·Bernhard SuterErich E Wanker
Jul 17, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Adrián López García De LomanaJordi Villà-Freixa
Aug 27, 2011·Bulletin of Mathematical Biology·W P Kelly, M P H Stumpf
Aug 17, 2011·Biological Procedures Online·Ying LiuSarah E Bondos
Feb 26, 2008·FEBS Letters·Eoghan D HarringtonPeer Bork
Feb 16, 2011·Current Opinion in Structural Biology·Amelie SteinPatrick Aloy
Oct 24, 2009·Current Opinion in Biotechnology·Masanori Arita
Jul 16, 2008·Current Opinion in Biotechnology·Bernhard SuterIgor Stagljar
May 13, 2008·Drug Discovery Today·Yin LiuHongyu Zhao
Nov 6, 2008·Molecular Systems Biology·B de ChasseyV Lotteau
Aug 7, 2008·Molecular Systems Biology·Jingshan ZhangEugene I Shakhnovich
May 23, 2012·Proteomics·Bernard A LiuPiers D Nash
Mar 2, 2011·Proteomics·Saurabh R Nirantar, Farid J Ghadessy
Jun 17, 2011·The Biochemical Journal·Ratnesh K SrivastavRainer Niedenthal
Apr 14, 2016·Chemical Reviews·Ozlem KeskinAttila Gursoy
Mar 20, 2008·Expert Opinion on Therapeutic Targets·Nicolas Lentze, Daniel Auerbach
May 31, 2011·Journal of Structural Biology·Anastassis PerrakisCarlo Petosa
Aug 26, 2014·Journal of Bioinformatics and Computational Biology·Alireza VazifedoostLimsoon Wong
Nov 14, 2015·PloS One·Maddalena DiluccaAndrea Giansanti

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Methods Mentioned

BETA
two-hybrid
laval
a

Software Mentioned

SCAFFOLD
INTEROLOG
PL
SCALED
MIXTURE
TPL

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