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Though we have demonstrated the value of biologically testing network predictions using 2D-DIGE and microarray data, many other types of screening tools could also be employed to test the functional coherence of predicted networks.
In our microarray data, many broiler and layer differentially expressed genes were classified into functional categories involved in metabolic processes.
R/Bioconductor provides a wide variety of visualizations for microarray data, many of which are available in Chipster.
Since violation of this assumption is relatively common in microarray data, many methods have been designed to circumvent its requirement [ 2, 12- 14].
In our microarray data, many kinase genes from OsCIPK (CBL-interacting protein kinase) and OsWNK (with no K = lysine) families were transcriptionally regulated in rice seedlings subjected to K+ deficiency (Additional file 6, 7).
Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have been developed for evaluating the significance of the observed differences in gene expression.
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This site provides deep and total access to many massive microarray data sets, many with a focus on the genetics and genomics of alcoholism (Bhave et al., 2007).
The microarray data from many experiments are uploaded to public databases such as GEO (Gene Expression Omnibus) [38], for other scientists to use in their research.
The microarray data from many experiments are often uploaded to public databases [40] such as GEO and ArrayExpress, for other scientists to use in their research.
Reactome only shows enzymes as nodes, which limits its applicability for the mapping of microarray data, since many enzymes exist as heteromers that are comprised of several proteins.
We wish to thank Dr. Oliver Dittrich-Breiholz from the Institute of Biochemistry, Hannover Medical School, Hannover, Germany and Dr Rainer Russ from Genedata AG, Basel, Switzerland for help in the generation and initial analysis of gene expression microarray data and many colleagues who generously shared their knowledge in the critical evaluation and interpretation of the results.
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