phenoDist Cell-based High-throughput Screening
Intensity(reporter) based screen Plate reader (intensity readout)
120 Cell seeding Mini. reaction
Image based screen
Microscope (image readout) Hit Identification
Negative control Sample Difference intensity screen 100 500 400
image screen ??
Image quantification
features features cell cell size shape int. ... size shape int. ...
1 50 0.3 650 ... 1 30 0.67 430 ... ?? 2 64 0.8 800 ... 2 40 0.4 788 ...
......
Dimension reduction Phenotypic distance
- 50 0.3 650 ... - 30 0.25 1200 ... 0.70
Distance Calculation Phenotypic Distance Methods
Computation steps
Tanaka 2005 Young 2008 Perlman 2004 Fuchs 2010 Loo 2007 1. Feature selection
Supervised SVM weight 2. Data Transformation PCA Factor analysis KS statistic classification vector
3. Distance calculation Phenotypic Distance via Classification
Negative control Sample
How similar/different are these two cell populations?
How easily can we separate the cell populations from each other, when they are mixed? Quality Control
Replicate correlation Replicate similarity Control separation 8 between replicates 25 RLUC 0.95 between non-replicates UBC CLSPN 20 0.90 6 0.85 15 4 0.80 Density Density 10 0.75
RLUC 2 5 0.70 Phenotypic strength (replicate 2) UBC CLSPN 0.65 0 Sample 0 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.4 0.5 0.6 0.7 0.8 0.9 1.0 0.6 0.7 0.8 0.9 Phenotypic strength (replicate 1) Phenotypic distance Phenotypic strength Hit Identification
0.95 PLK1 0.90 0.85 0.80 0.75 RLUC 0.70 Phenotypic strength (replicate 2) UBC
CLSPN 0.95 0.65 Sample COPB2 0.60 0.65 0.70 0.75 0.80 0.85 0.90 Phenotypic strength (replicate 1) 0.90 RLUC 0.85
UBC 0.80 0.80 0.85 0.90 AKAP7 PANK4 CLSPN Hit Identification with Phenotypic Similarity
RAC1 PINK1 MAP3K3 PIK3R4 PRPSAP2
GK MRC2 PRKY PRKDC MPZL1
MGC5601 PDGFRB PANK4 PRKCH MAPKAPK3
PAK6 PACE-1 NTRK1 PMVK EXOSC10
PLK1 PKM2 PKIB CDKL5 GUCY2D
GTF2H1 AKAP7 GCK ADRBK1 ADRB2
COPB2 ERBB4 ABI1 TESK2 STK39 Hit Identification with Phenotypic Similarity
RAC1 PINK1 MAP3K3 PIK3R4 PRPSAP2
GK MRC2 PRKY PRKDC MPZL1
MGC5601 PDGFRB PANK4 PRKCH MAPKAPK3
PAK6 PACE-1 NTRK1 PMVK EXOSC10
PLK1 PKM2 PKIB CDKL5 GUCY2D
GTF2H1 AKAP7 GCK ADRBK1 ADRB2
COPB2 ERBB4 ABI1 TESK2 STK39 Hit Identification with Phenotypic Similarity
RAC1 PINK1 MAP3K3 PIK3R4 PRPSAP2
GK MRC2 PRKY PRKDC MPZL1
MGC5601 PDGFRB PANK4 PRKCH MAPKAPK3
PAK6 PACE-1 NTRK1 PMVK EXOSC10
PLK1 PKM2 PKIB CDKL5 GUCY2D
GTF2H1 AKAP7 GCK ADRBK1 ADRB2
COPB2 ERBB4 ABI1 TESK2 STK39 Hit Identification with Phenotypic Similarity
CDKL5 ABI1
PKM2 RAC1 MAP3K3 GK COPB2 AKAP7 NTRK1
PMVK
MRC2 PINK1 MPZL1 ADRBK1 PLK1
PIK3R4 ACAD10 PDGFRB PRPSAP2 TESK2 GTF2H1 Hit Identification with Phenotypic Similarity
RAC1 MAP3K3 GK
CDKL5 ABI1
PKM2 RAC1 MAP3K3 GK COPB2 AKAP7 NTRK1
PMVK
MRC2 PINK1 MPZL1 ADRBK1 PLK1
PIK3R4 ACAD10 PDGFRB PRPSAP2 TESK2 GTF2H1
PLK1 PMVK MPZL1 MRC2 TESK2 ADRBK1
PIK3R4 PDGFRB PRPSAP2 ACAD10 PINK1 GTF2H1 Future Development
Expand to compound screening analysis e.g., dosage responsive curve, IC50 value
1.0 0.9 0.8 0.7
0.6 Phenotypic strength 0.5 Increasing concentration Developed by
Xian Zhang Greg Pau Michael Boutros Wolfgang Huber
Division Signaling and Functional Genomics Genome Biology Unit German Cancer Research Center EMBL