Increasing Confidence of Protein-Protein Interactomes

High-throughput experimental methods, such as yeast-two-hybrid and phage display, have fairly high levels of false positives (and false negatives). Thus the list of protein-protein interactions detected by such experiments would need additional wet laboratory validation. It would be useful if the li...

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Published inGenome Informatics Vol. 17; no. 2; pp. 284 - 297
Main Authors Chen, Jin, Chua, Hon Nian, Hsu, Wynne, Lee, Mong-Li, Ng, See-Kiong, Saito, Rintaro, Sung, Wing-Kin, Wong, Limsoon
Format Journal Article
LanguageEnglish
Published Japan Japanese Society for Bioinformatics 2006
Subjects
Alternative Splicing
Amino Acid Motifs
Amino Acid Sequence
Animals
Computational Biology - methods
DNA, Complementary
Gene Expression
graph mining
Humans
Mice
network motif
Promoter Regions, Genetic
Protein Binding
Protein Interaction Mapping - methods
protein-protein interaction network
Proteins - chemistry
Proteins - classification
Proteins - genetics
Proteins - metabolism
Reproducibility of Results
Sequence Analysis, Protein
Transcription Initiation Site
Transcription, Genetic
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Summary:High-throughput experimental methods, such as yeast-two-hybrid and phage display, have fairly high levels of false positives (and false negatives). Thus the list of protein-protein interactions detected by such experiments would need additional wet laboratory validation. It would be useful if the list could be prioritized in some way. Advances in computational techniques for assessing the reliability of protein-protein interactions detected by such high-throughput methods are reviewed in this paper, with a focus on techniques that rely only on topological information of the protein interaction network derived from such high-throughput experiments. In particular, we discuss indices that are abstract mathematical characterizations of networks of reliable protein-protein interactions-e.g., “interaction generality”(IG), “interaction reliability by alternatve pathways”(IRAP), and “functional similarity weighting”(FSWeight). We also present indices that are based on explicit motifs associated with true-positive protein interactions-e.g., “new interaction generality”(IG2) and “meso-scale motifs”(NeMoFinder).
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ISSN:0919-9454
2185-842X
DOI:10.11234/gi1990.17.2_284