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This annotation file can be opened with the Blast2GO software and by uploading each list of strain-specific varying genes, Blast2GO functions can be used to interrogate data for significant functional differences between isolates at the genome level, and to obtain the functional profiling of the genomic alterations or to locate mutated genes in metabolic pathways.
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Computer aided software such as NVivo (a qualitative data analysis tool that helps to organise and analyse unstructured, i.e. non-numerical data) will be used to interrogate the data at different levels.
From the database, multiple software packages have been used to interrogate the data [13, 14].
Benthic community monitoring strategies and descriptors applied to UK OWFs were used to interrogate real data variability in the marine environment.
To identify which mRNAs are differentially expressed, limma and fspma packages were used to interrogate the data [ 49- 51].
The prognostic algorithm was used to interrogate genomic data from a series of patients treated with adjuvant chemotherapy.
They did, however, belong to the core group of genes that were enriched when a micromass culture gene set was used to interrogate the DEX data.
Second, a batch query of up to 600 genes can be used to interrogate categories of data from different screens to provide a summary of each gene over the large-scale screening projects within the database.
This finding was only made possible by the ease with which GSMA can be used to interrogate gene expression data comprehensively using very large gene sets (the TransFac gene set contains 445 separate gene lists), a task that just a short time ago would have been prohibitive for a moderately sized laboratory solely for the purposes of exploration.
This program, referred to as the Common set of v- Src Regulated genes or CSR genes, was then used to interrogate several independent tumor data sets with corresponding clinical information.
Most importantly, the availability of this information has led to a technological boom, with the development of high-throughput methods that could be used to interrogate the wealth of data available in the human genome and transcriptome.
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