title: Automatic identification of subcellular phenotypes on human cell arrays.
abstract: Light microscopic analysis of cell morphology provides a high-content readout of cell function and protein localization. Cell arrays and microwell transfection assays on cultured cells have made cell phenotype analysis accessible to high-throughput experiments. Both the localization of each protein in the proteome and the effect of RNAi knock-down of individual genes on cell morphology can be assayed by manual inspection of microscopic images. However, the use of morphological readouts for functional genomics requires fast and automatic identification of complex cellular phenotypes. Here, we present a fully automated platform for high-throughput cell phenotype screening combining human live cell arrays, screening microscopy, and machine-learning-based classification methods. Efficiency of this platform is demonstrated by classification of eleven subcellular patterns marked by GFP-tagged proteins. Our classification method can be adapted to virtually any microscopic assay based on cell morphology, opening a wide range of applications including large-scale RNAi screening in human cells.
authors.affiliation: Intelligent Bioinformatics Systems, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Conrad
authors.forename: Holger
authors.initials: H
authors.lastname: Erfle
authors.forename: Patrick
authors.initials: P
authors.lastname: Warnat
authors.forename: Nathalie
authors.initials: N
authors.lastname: Daigle
authors.forename: Thomas
authors.initials: T
authors.lastname: Lörch
authors.forename: Jan
authors.initials: J
authors.lastname: Ellenberg
authors.forename: Rainer
authors.initials: R
authors.lastname: Pepperkok
authors.forename: Roland
authors.initials: R
authors.lastname: Eils
mesh_terms: D016477:Artifacts; D001943:Breast Neoplasms / Q000145:classification* / Q000235:genetics / Q000473:pathology; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics; D049452:Green Fluorescent Proteins; D006801:Humans; D042541:Intracellular Space / Q000145:classification; D008164:Luminescent Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010641:Phenotype; D012107:Research Design / Q000592:standards; D014162:Transfection / Q000295:instrumentation / Q000379:methods
chemical_list: D008164:Luminescent Proteins; D049452:Green Fluorescent Proteins