H-AM: p-value, penetrance, cell count and well count data for each marker and screen type
AN-BG: total cell count, total well count, combined mean penetrance, penetrance SD data for
each marker
BH-DE: data on phenotype fractions for each phenotype and screen type
DF-GK: combined phenotype fraction, and phenotype fraction SD, (stringent) SPM calls for
each phenotype
Cell Cycle Omics
Legend
GE: Gene Expression
TE: Translational Efficiency
PA: Protein Abundance
Loc: Protein Localization
R1, R2 and R3: Biological replicate 1, 2 and 3
Columns
A-B: Gene information (ORF, standard name)
C-M: Gene Expression hit call and data for each cell cycle phase across two biological replicates
N-X: Translational Efficiency hit call and data for each cell cycle phase across two biological replicates
Y-AQ: Protein Abundance hit call and data for each cell cycle phase across three biological replicates
AR: Protein Localization hit call
AS-PX: Protein Localization data for each compartment and cell cycle phase across three
biological replicates (columns named [compartment] [phase] (R[replicate]))
LOCscore_ensLOC: quantitative measurement of localization in each ensLOC screen
LOCscore_DeepLoc: quantitative measurement of localization in each DeepLoc screen
Zscore: quantitative localization changes in sub-cellular compartments
Abundance: GFP intensity measures of the protein in each screen
Columns
[screen]_Mean - Mean Cell GFP Intensity (1e-4)
[screen]_Stdev - Standard Deviation (1e-4)
[screen]_Change - Intensity Change (Log2)
Notes
strains with signal below threshold were not filtered from the dataset
ensLOC and DeepLoc scores that are less than 0.05 are rounded-down to 0
DUB Biology – Proteome Dynamics
Legend
WT: wild type
UBP2, UBP14, UBP2UBP14:ubp2Δ, ubp14Δ and ubp2Δ ubp14Δ mutants
R1, R2: biological replicates 1 and 2; R1 & R2: both replicates combined
*: significant value (highlighted in the tables on the website)
N/A: no data for that replicate and strain
Sheets (four per gene)
[gene] - CellCount: number of cells analysed
[gene] - Abundance: mean and standard deviation of cell GFP intensity, and intensity change
(Log2) relative to wild type
[gene] - LocScore: DeepLoc localization score for each compartment (rows)
[gene] - LocChange: localization change (T-score) for each compartment (rows)
Columns
CellCount, Abundance and LocScore sheets: B-E: R1, F-I: R2, J-M: R1 & R2; each with WT,
UBP2, UBP14 and UBP2UBP14
LocChange sheet: B-F: R1, G-K: R2, L-P: R1 & R2; each with the comparisons UBP2_WT,
UBP14_WT, UBP2UBP14_WT, UBP2UBP14_UBP2 and UBP2UBP14_UBP14 (mutant vs control)
Localization compartments (21)
Actin
Bud Neck
Bud Site
Cell Periphery
Cytoplasm
Cytoplasmic Foci
Eisosomes
Endoplasmic Reticulum
Endosome
Golgi
Lipid Particles
Mitochondria
Mitotic Spindle
None
Nuclear Periphery
Nuclear Periphery Foci
Nucleolus
Nucleus
Peroxisomes
Vacuole
Vacuole Periphery
Intracellular Organization Dynamics
Legend
Penetrance: percentage of cells with morphologically abnormal structure
TP0-TP24: timepoints 0 to 24 hours
Columns
A: Gene (one row per gene)
B-GH: Penetrance for each subcellular structure (marker protein) at each timepoint; 9 columns
per structure, named [structure] ([marker])_TP[timepoint]