CellProfiler Analyst: data exploration and analysis software for complex image-based screens

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Abstract

Background

Image-based screens can produce hundreds of measured features for each of hundreds of millions of individual cells in a single experiment.

Results

Here, we describe CellProfiler Analyst, open-source software for the interactive exploration and analysis of multidimensional data, particularly data from high-throughput, image-based experiments.

Conclusion

The system enables interactive data exploration for image-based screens and automated scoring of complex phenotypes that require combinations of multiple measured features per cell.

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Most cited references 40

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Genes required for mitotic spindle assembly in Drosophila S2 cells.

Gohta Goshima, Roy Wollman, Sarah Goodwin … (2007)

The formation of a metaphase spindle, a bipolar microtubule array with centrally aligned chromosomes, is a prerequisite for the faithful segregation of a cell's genetic material. Using a full-genome RNA interference screen of Drosophila S2 cells, we identified about 200 genes that contribute to spindle assembly, more than half of which were unexpected. The screen, in combination with a variety of secondary assays, led to new insights into how spindle microtubules are generated; how centrosomes are positioned; and how centrioles, centrosomes, and kinetochores are assembled.

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Statistical practice in high-throughput screening data analysis.

Nathalie Malo, James Hanley, Sonia Cerquozzi … (2006)

High-throughput screening is an early critical step in drug discovery. Its aim is to screen a large number of diverse chemical compounds to identify candidate 'hits' rapidly and accurately. Few statistical tools are currently available, however, to detect quality hits with a high degree of confidence. We examine statistical aspects of data preprocessing and hit identification for primary screens. We focus on concerns related to positional effects of wells within plates, choice of hit threshold and the importance of minimizing false-positive and false-negative rates. We argue that replicate measurements are needed to verify assumptions of current methods and to suggest data analysis strategies when assumptions are not met. The integration of replicates with robust statistical methods in primary screens will facilitate the discovery of reliable hits, ultimately improving the sensitivity and specificity of the screening process.

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Shugoshin collaborates with protein phosphatase 2A to protect cohesin.

Tomoya S. Kitajima, Takeshi Sakuno, Kei-ichiro Ishiguro … (2006)

Sister chromatid cohesion, mediated by a complex called cohesin, is crucial--particularly at centromeres--for proper chromosome segregation in mitosis and meiosis. In animal mitotic cells, phosphorylation of cohesin promotes its dissociation from chromosomes, but centromeric cohesin is protected by shugoshin until kinetochores are properly captured by the spindle microtubules. However, the mechanism of shugoshin-dependent protection of cohesin is unknown. Here we find a specific subtype of serine/threonine protein phosphatase 2A (PP2A) associating with human shugoshin. PP2A colocalizes with shugoshin at centromeres and is required for centromeric protection. Purified shugoshin complex has an ability to reverse the phosphorylation of cohesin in vitro, suggesting that dephosphorylation of cohesin is the mechanism of protection at centromeres. Meiotic shugoshin of fission yeast also associates with PP2A, with both proteins collaboratively protecting Rec8-containing cohesin at centromeres. Thus, we have revealed a conserved mechanism of centromeric protection of eukaryotic chromosomes in mitosis and meiosis.

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Author and article information

Journal

Journal ID (nlm-ta): BMC Bioinformatics

Title: BMC Bioinformatics

Publisher: BioMed Central

ISSN (Electronic): 1471-2105

Publication date Collection: 2008

Publication date (Electronic): 15 November 2008

Volume: 9

Page: 482

Affiliations

[1 ]Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

[2 ]Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA

[3 ]Computer Sciences and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA

[4 ]Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA

Article

Publisher ID: 1471-2105-9-482

DOI: 10.1186/1471-2105-9-482

PMC ID: 2614436

PubMed ID: 19014601

SO-VID: 41ca1dbc-a229-48f2-88b9-e6b6430e8abc

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

CellProfiler Analyst: data exploration and analysis software for complex image-based screens

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Abstract

Background

Results

Conclusion

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Most cited references 40

Genes required for mitotic spindle assembly in Drosophila S2 cells.

Statistical practice in high-throughput screening data analysis.

Shugoshin collaborates with protein phosphatase 2A to protect cohesin.

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