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. 2018 Jan 5;17(1):722-726.
doi: 10.1021/acs.jproteome.7b00572. Epub 2017 Oct 31.

BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data

Devin K Schweppe  1 , Edward L Huttlin  1 , J Wade Harper  1 , Steven P Gygi  1
Affiliations

BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data

Devin K Schweppe et al. J Proteome Res. .

Abstract

The development of large-scale data sets requires a new means to display and disseminate research studies to large audiences. Knowledge of protein-protein interaction (PPI) networks has become a principle interest of many groups within the field of proteomics. At the confluence of technologies, such as cross-linking mass spectrometry, yeast two-hybrid, protein cofractionation, and affinity purification mass spectrometry (AP-MS), detection of PPIs can uncover novel biological inferences at a high-throughput. Thus new platforms to provide community access to large data sets are necessary. To this end, we have developed a web application that enables exploration and dissemination of the growing BioPlex interaction network. BioPlex is a large-scale interactome data set based on AP-MS of baits from the human ORFeome. The latest BioPlex data set release (BioPlex 2.0) contains 56 553 interactions from 5891 AP-MS experiments. To improve community access to this vast compendium of interactions, we developed BioPlex Display, which integrates individual protein querying, access to empirical data, and on-the-fly annotation of networks within an easy-to-use and mobile web application. BioPlex Display enables rapid acquisition of data from BioPlex and development of hypotheses based on protein interactions.

Keywords: AP−MS; BioPlex; PHP/MySQL; data visualization; graph display; network communities; protein complexes; protein interactions; term enrichment; web application.

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Conflict of interest statement

The authors declare the following competing financial interest(s): S.P.G is a consultant for Biogen, Inc.

Figures

Figure 1.
Figure 1.
Overview of BioPlex Display and general information on the graph representations. The BioPlex interactome network consisting of bait–prey interactions as well as annotations and additional information is stored in MySQL databases. These databases are queried in real time with the user accessing the site to generate graph representations of the protein interaction network for a specific input. (The example given is for the retromer complex subunit VPS29.)
Figure 2.
Figure 2.
Network exploration and hypothesis development for the uncharacterized protein C12orf59. (A) Default representation of a queried protein interaction subnetwork. Proteins used as baits at some point in the BioPlex project are shown as green circles. Proteins only identified as preys are shown as blue diamonds. The original protein query is highlighted in purple, and its annotation as either a BioPlex bait (circle) or a prey-only protein (diamond) is retained. (B) On the basis of previous spectral-counting data for HEK293T cells, the relative protein abundance for each protein in the C12orf59 network is shown as a gradient from high expression (red) down to no detection (yellow). (C) For each protein interaction network, gene ontology (GO) annotation enrichment is calculated. Proteins belonging to specific GO annotation groups can be highlighted. Phosphatidylinositol 3-kinase complex proteins (orange nodes) were observed to be enriched in the C12orf59 interaction network (Fisher’s Exact test adjusted p-value: 2.30 × 10−8).
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