TheCellVision | Endocytosis Supplemental Files

Table EV1 List of CellProfiler features and positive controls for each marker and screen type, information on training set size and 2NN accuracy. Related to Figure 1, Figure EV1, and Figure EV2. TableEV1.xlsx
Table EV2 Main results table. Contains data on phenotype, penetrance and threshold information for each screened mutant strain, and consensus morphology mutant lists. Related to Figure 1, Figure 2, Figure 3, and Figure 5. TableEV2.xlsx
Table EV3Enrichment results of the morphology mutants. Related to Figure 2, and Figure EV3. TableEV3.xlsx
Table EV4 Protein complex, localization, cell size and marker abundance standards. Related to Figure 2, Figure 3, Figure EV3, Figure EV4, and Figure EV5. TableEV4.xlsx
Table EV5 Analysis of phenotype similarity and the common morphology mutants of endocytic compartment phenotypes. Related to Figure 3, Figure EV4. TableEV5.xlsx
Table EV6 Endocytic internalization defect comparison of the mutant phenotypes. Related to Figure EV4. TableEV6.xlsx
Table EV7 Within-complex phenotype profile similarity. Related to Figure EV5. TableEV7.xlsx
Table EV8 Factors contributing to incomplete penetrance. Related to Figure 5, Figure 6, Figure EV6. TableEV8.xlsx

Raw and processed images were deposited to the Image Data Resource (https://idr.openmicroscopy.org) under accession number idr0078

For each screened gene, we built a profile with its 17 specific phenotype fractions (phenotype fraction data is provided in Table S2). For genes with several screened alleles, we used the mean specific phenotype fraction across alleles (Additional file 1). For each pair of genes we calculated the Pearson correlation coefficient (PCC) between their profiles (Additional file 2). Strains with incomplete profiles (missing data for any of the 4 markers) were excluded from the analysis (Additional file 3).
Additional File 1 Mean Phenotype Profile
File with 18 columns: ORF, fractions for 17 mutant phenotypes
Mean_phenotype_profile.csv
Additional File 2 List of pairwise profile similarities for all screened genes (13,999,986 rows)
File with 3 columns, without header: ORF1 | ORF2 | PCC
phenotype_PCCs.full_profiles.csv.bz2
Additional File 3 Removed ORFs
List of ORFs that have been deleted from SGD and were excluded from the gene feature enrichment analysis.
Removed_ORFs.csv
Additional File 4 Training sets for the endocytic compartment phenotypes training_sets.tar.gz