Publication Date:
2019-02-13
Description:
Motivation Network analysis and unsupervised machine learning processing of single-molecule localization microscopy of caveolin-1 (Cav1) antibody labeling of prostate cancer cells identified biosignatures and structures for caveolae and three distinct non-caveolar scaffolds (S1A, S1B and S2). To obtain further insight into low-level molecular interactions within these different structural domains, we now introduce graphlet decomposition over a range of proximity thresholds and show that frequency of different subgraph (k = 4 nodes) patterns for machine learning approaches (classification, identification, automatic labeling, etc.) effectively distinguishes caveolae and scaffold blobs. Results Caveolae formation requires both Cav1 and the adaptor protein CAVIN1 (also called PTRF). As a supervised learning approach, we applied a wide-field CAVIN1/PTRF mask to CAVIN1/PTRF-transfected PC3 prostate cancer cells and used the random forest classifier to classify blobs based on graphlet frequency distribution (GFD). GFD of CAVIN1/PTRF-positive (PTRF+) and -negative Cav1 clusters showed poor classification accuracy that was significantly improved by stratifying the PTRF+ clusters by either number of localizations or volume. Low classification accuracy (
Print ISSN:
1367-4803
Electronic ISSN:
1460-2059
Topics:
Biology
,
Computer Science
,
Medicine
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