web cellHTS2: a web-application for the analysis of high-throughput screening data.
BACKGROUND
The analysis of high-throughput screening data sets is an expanding field in bioinformatics. High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify relevant phenotypic hits. Large-scale RNAi screens are frequently used to identify novel factors that influence a broad range of cellular processes, including signaling pathway activity, cell proliferation, and host cell infection. Here, we present a web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS2.


RESULTS
The software guides the user through the configuration steps that are required for the analysis of single or multi-channel experiments. The web-application provides options for various standardization and normalization methods, annotation of data sets and a comprehensive HTML report of the screening data analysis, including a ranked hit list. Sessions can be saved and restored for later re-analysis. The web frontend for the cellHTS2 R/Bioconductor package interacts with it through an R-server implementation that enables highly parallel analysis of screening data sets. web cellHTS2 further provides a file import and configuration module for common file formats.


CONCLUSIONS
The implemented web-application facilitates the analysis of high-throughput data sets and provides a user-friendly interface. web cellHTS2 is accessible online at http://web-cellHTS2.dkfz.de. A standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 can be downloaded from the web cellHTS2 page. web cellHTS2 is freely distributed under GPL.
Pelz
Oliver
O
German Cancer Research Center (DKFZ), Div Signaling and Functional Genomics and University of Heidelberg, Faculty of Medicine Mannheim, Dept Cell and Molecular Biology, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.
Gilsdorf
Moritz
M
Boutros
Michael
M
D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D023281:Genomics / Q000379:methods*; D057166:High-Throughput Screening Assays; D020407:Internet; D034622:RNA Interference; D012984:Software; D014584:User-Computer Interface
J Biomol Screen. 1999;4(2):67-73
10838414
Nat Rev Mol Cell Biol. 2006 Mar;7(3):177-87
16496020
Cell. 2006 May 5;125(3):523-33
16678096
Cancer Cell. 2009 Apr 7;15(4):328-40
19345331
J Biomol Screen. 2003 Dec;8(6):634-47
14711389
Genome Biol. 2004;5(10):R80
15461798
Genome Biol. 2006;7(7):R66
16869968
Nucleic Acids Res. 2007 Jan;35(Database issue):D492-7
17135194
Bioinformatics. 2009 Mar 1;25(5):678-9
19168909
Nat Biotechnol. 2006 Feb;24(2):167-75
16465162
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D489-94
16381918
J Biomol Screen. 2008 Feb;13(2):149-58
18216396
Nature. 2006 Feb 2;439(7076):604-7
16452979
Nat Methods. 2009 Aug;6(8):569-75
19644458
Nat Rev Genet. 2008 Jul;9(7):554-66
18521077