ProHits-viz: a suite of web tools for visualizing interaction proteomics data

Knight, James D.R.; Choi, Hyungwon; Gupta, Gagan D.; Pelletier, Laurence; Raught, Brian; Nesvizhskii, Alexey I.; Gingras, Anne‐Claude

doi:10.1038/nmeth.4330

Cited by 169 publications

(172 citation statements)

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“…To get a more global and quantitative visualization of the preys identified by each RC-APEX bait, we generated dot plots using the ProHits-viz tool (Knight et al, 2017) (Figure 5A-D). The color of each prey 'dot' is dependent on the Normalized Spectral Abundance Factor (NSAF) log 2 (FoldChange) for each bait compared to the control samples (see Figure 5 key).…”

Section: Identification and Characterization Of Rc-apex High-confidenmentioning

confidence: 99%

“…The PLA assay confirmed that Pav interacts with itself, as indicated by fluorescent foci throughout egg chambers and at ring canals ( Figure 6A, top panel) compared to . Dotplots were generated using ProHits-viz (Knight et al, 2017), and high-confidence preys (SAINTscore ≥ 0.8) are outlined in yellow. Note that each RC-APEX bait identified mostly distinct high-confidence preys (compare columns).…”

Section: Validation Of Rc-apex High-confidence Preys By Proximity Ligmentioning

confidence: 99%

“…The ProHits-viz tool (Knight et al, 2017) was used to generate dotplots to visualize proteomics data for any high-confidence prey across all four RC-APEX bait samples. The color of each prey 'dot' was dependent on the NSAF log 2 (FoldChange) for each bait compared to the control samples.…”

Section: Generation Of Dot Plots and Heatmaps With Prohits-vizmentioning

confidence: 99%

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Proximity labeling reveals novel interactomes in live Drosophila tissue

Mannix

Starble

Kaufman

et al. 2019

Preprint

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Gametogenesis is dependent on intercellular communication facilitated by stable intercellular bridges connecting developing germ cells. During Drosophila oogenesis, intercellular bridges (referred to as ring canals) have a dynamic actin cytoskeleton that drives their expansion to a diameter of 10µm. While multiple proteins have been identified as components of ring canals (RCs), we lack a basic understanding of how RC proteins interact together to form and regulate the RC cytoskeleton. We optimized a procedure for proximity-dependent biotinylation in live tissue using the APEX enzyme to interrogate the RC interactome. APEX was fused to four different RC components (RC-APEX baits) and 55 unique high-confidence preys were identified. The RC-APEX baits produced almost entirely distinct interactomes that included both known RC proteins as well as uncharacterized proteins. The proximity ligation assay was used to validate close-proximity interactions between the RC-APEX baits and their respective preys. Further, an RNAi screen revealed functional roles for several high-confidence prey genes in RC biology. These findings highlight the utility of enzyme-catalyzed proximity labeling for protein interactome analysis in live tissue and expand our understanding of RC biology. Summary StatementHere, we optimized a procedure for enzyme-catalyzed proximity labeling in live Drosophila ovary tissue to interrogate the Drosophila ring canal protein interactome.

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Section: Identification and Characterization Of Rc-apex High-confidenmentioning

confidence: 99%

Section: Validation Of Rc-apex High-confidence Preys By Proximity Ligmentioning

confidence: 99%

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Proximity labeling reveals novel interactomes in live Drosophila tissue

Mannix

Starble

Kaufman

et al. 2019

Preprint

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“…AvgIntensity, average intensity (generated from SAINTexpress); BFDR, Bayesian false discovery rate. Dot plot was generated by Prohits-Viz 84 .…”

Section: Fig 5 Proximity Interactions Of the Central Prey Clustermentioning

confidence: 99%

Definition of the fibroblast adhesome using multiplexed proximity biotinylation

Chastney

Lawless

Humphries

et al. 2020

Preprint

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Integrin adhesion complexes (IACs) bridge the extracellular matrix to the actin cytoskeleton and transduce signals in response to both chemical and mechanical cues. The composition, interactions, stoichiometry and topological organisation of proteins within IACs are not fully understood. To address this gap, we used multiplexed proximity biotinylation (BioID) to generate an in situ, proximity-dependent adhesome in mouse pancreatic fibroblasts. Integration of the interactomes of 16 IACassociated baits revealed a network of 147 proteins with 361 proximity interactions.Candidates with underappreciated roles in adhesion were identified, in addition to established IAC components. Bioinformatic analysis revealed five clusters of IAC baits that link to common groups of prey, and which therefore may represent functional modules. The five clusters, and their spatial associations, are consistent with current models of IAC interaction networks and stratification. This study provides a resource to examine proximal relationships within IACs at a global level.

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“…Data Visualization -Dot plots and heat maps were generated using ProHits-viz (prohitsviz.lunenfeld.ca) (46). Prey proteins identified as high confidence proximal interactors (FDR ≤1%) are provided in Supplemental Table S1-4; In ProHits-viz, once a prey passes the ≤1% FDR threshold with one bait, all its quantitative values across all baits are recovered, and the respective SAINT FDR is represented as the edge color intensity.…”

Section: Publication: Vbioidmcp1mentioning

confidence: 99%