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The systematic integration of gene sets, the protein interaction network, and microarray gene expression data offers us three main advantages: First, it enables us to sufficiently utilize the gene co-expression information provided by the microarray data, which is believed to be more informative than expression changes of individual genes for target gene identification.
The analysis of ZmHsfs expression profiles was accomplished by searching the maize dbEST database and finding expression information provided at the Web sites.
The second method, developed by Jiang et al. [ 30], refined Hu et al.'s result using the TF binding and gene expression similarity information provided by ChIP-chip data and gene expression data, respectively.
For more interactions see Figure 2. Assuming that genes with similar tissue-specific expression patterns are likely to share common regulatory elements, we clustered co-expressed genes according to their tissue-specific expression using information provided by TiProd database [ 51].
The information provided by gene expression profiling may contribute to the design of molecular mechanism-based strategies for cancer prevention and/or treatment.
Conversely, information provided by gene expression data may be exploited by the proposed algorithm in conjunction with knockout fitness data to synergistically improve final inference results.
The remaining 80% of the genes with significant isoforms did not show significant changes at the gene level, which represents the unique information provided by isoform expression profiles.
Multivariate analysis examined whether the information provided by GP88 expression duplicated or was additive to that provided by conventional risk factors, such as age, ethnicity, progesterone receptor (PR) expression, tumor size, tumor grade, disease stage, lymph node status and treatments.
The first component of the pipeline is ASPic, a method to predict alternative splicing isoforms expressed by a gene and their exon-intron organization at the genomic level through the information provided by available expression data, mostly EST sequences [ 26, 27].
The development of new proteomics assays, and the synthesis of existing knowledge in cellular signaling pathways with information provided by gene expression studies, will be necessary to build up a complete arthritis-related regulatory network and to unravel the mechanisms involved in the development and progression of autoimmune arthritis.
In addition to the new information provided by those gene expression patterns that have not been reported in adults previously, there is also significant potential to confirm and extend our knowledge of those genes with existing expression data, because the methodology used provides high resolution for a wide range of tissues.
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