Extended Data Fig. 9: Analysis module at humancellmap.org.
From: A proximity-dependent biotinylation map of a human cell
a, Screenshot of the analysis report for the bait PIK3R1. Red circles indicate the following (1) Baits from the humancellmap are sorted from most similar to least similar as calculated by the Jaccard distance. (2) The ten most similar baits to the query in the humancellmap. (3) The average spectral counts for each prey averaged across all baits in the humancellmap database. (4) Expected localizations of the ten most similar baits. (5) Overlap or similarity metrics between the query bait and the top ten most similar baits in the humancellmap. The distance is the Jaccard distance, with a score of 0 for complete prey overlap and 1 for no overlap. The intersection refers to the number of shared preys, and the union refers to the combined number of preys between the query and the indicated bait. (6) The most specific preys for the query. The specificity score is calculated as the fold enrichment of a prey in the query relative to the average across the humancellmap baits used for the comparison. (7) The specificity score calculated against the top ten most similar baits to the query. (8) The specificity score calculated against all baits in the humancellmap. (9) Links to open the heat map or specificity plots at the interactive viewer at ProHits-viz39. (10) Links for data downloads. b, Specificity plot for RNGTT showing the control-subtracted spectral counts versus the specificity score (calculation of the specificity score is described in the Methods). RNGTT is a nuclear protein involved in mRNA capping previously profiled by BioID7. Humancellmap analysis reported a nuclear localization, with bait-specific interactions including several RNA polymerase II subunits and components of the catalytic subunit of the PP4 phosphatase, as previously reported57,58. c, Exploratory analysis of FAM171A1 reveals links to the cytoskeleton. FAM171A1 was predicted by our NMF and SAFE analyses to localize to the cell junction and plasma membrane. Consistent with this prediction, its BioID profile when screened as a bait was most similar to junctional and plasma membrane baits, whereas bait-specific preys included several cytoskeletal proteins, in line with a previous study59 that reported a reduction of actin stress fibres after knockdown of FAM171A1. d, Specificity plot of MTFR2 showing the high specificity of proteins involved in mitochondrial dynamics. MTFR2 was associated with the mitochondrial outer membrane and peroxisome as a prey protein, with a weak signature at the mitochondrial inner membrane or mitochondrial intermembrane space. When profiled as a bait, the analysis module reports that it is most similar to peroxisomal baits, followed by mitochondrial outer and inner membrane baits, supporting its predicted localization. Interactions with MTFR1, SLC25A46 and VPS13D were found to be highly specific to MTFR2, consistent with the mitochondrial fragmentation previously observed after overexpression of GFP–MTFR260. e, BRD3 relocalization after JQ1 treatment. BirA-tagged BRD3 was treated with vehicle or JQ1 for 24 h (data from ref. 25) and analysed using the analysis module at humancellmap.org. The Jaccard indices (1 − Jaccard distance) for the top 20 most similar baits were used to create networks in Cytoscape41 using an edge-weighted spring-embedded layout. Humancellmap baits are coloured on the basis of their expected localization to chromatin or the nucleolus.
