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To compare the effectiveness of performing integrative GNPA with the new PAGER database, we set up a control experiment to examine the gene regulatory network that can be constructed following microarray data analysis.
Following microarray, data were extracted and processed using the DEVA software (NimbleGen), where alignment, normalization of the ratios and segmentation analysis were performed.
Following microarray data analysis, a list of preferentially expressed genes in both microfilariae species was generated with a false discovery rate estimate of 5% and a signal intensity ratio of 2 or higher in either species.
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The following six benchmark microarray data sets have been extensively studied and used in our experiments to compare the performances of our methods with others.
Bioinformatic analysis of microarray data following TBI identified key molecular pathways and networks associated with neural injury following TBI.
Tissue-enriched genes were identified by the following procedures: The microarray data were subjected to preliminary screening with a selection threshold of false discovery rate (FDR) less than 5% using a multiclass method in the SAM software.
In preprocessing of the microarray data, following hierarchical clustering of the samples, three outliers were removed (see Text S1), and filtering of low-intensity probes left 14,831 and 14,653 genes in the CF and conidia experiments, respectively.
The datasets were profiled with Affymetrix Human Genome U133A Arrays and we reprocessed the microarray data following identical procedures as described above.
Examination of microarray data following Matrigel-induced deactivation of HSC revealed a significant down-regulation of myocardin, an important transcriptional regulator in smooth and cardiac muscle development.
The TM4 suite of tools consists of the following four major applications: Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS), Multiexperiment Viewer (MeV).
Based on time-course microarray data following primary and secondary infection of zebrafish by Candida albicans, we constructed two intracellular protein protein interaction (PPI) networks for primary and secondary responses of the host.
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