Stopwords were removed to reduce the excess of noise in the lists of candidate terms.
This software interactively assembles data from different experiments and produces lists of candidate genes according to patterns of gene expression.
For the semi-automatic term extraction in this project, the NSP package was used to generate lists of candidate terms (unigrams, bigrams, trigrams, quadrigrams, and pentagrams).
In the sequence, such lists of candidate terms were manually cleaned by a linguist, as well as a posteriori validation of the candidates by a domain expert.
Often investigations of this kind result in long lists of candidate interactors.
Results from the different studies make it possible to investigate to what degree genetic background or inbreeding influence the lists of candidate genes detected.
The recent compilation of predicted RXLR effectors aided our work by providing lists of candidate genes that were often overlooked by gene annotation programs.
Although genetic interaction, expression profiling and chromatin binding approaches can provide lists of candidate TGs, they each suffer from disadvantages such as high cost, technical limitations, inability to detect direct TGs, and prohibitive numbers of conditions to test [6].
However, results from computational methods for determining CRMs (e.g. Cluster-Buster [30] and CisModule [31]) are rarely reported for ChIP-Seq data, because they are too computationally intensive or return long lists of candidate modules that are challenging to assess.
Ideally, computational approaches to mine entire genomes for TFBSs and CRMs would generate highly accurate lists of candidate TGs that can be taken directly to in vivo biological validation.
Application of the methods established in this study for refining lists of candidate genes obtained through transcriptome analyses, including the identification of likely functional paralogs among hypothesized paralogs, will allow for more efficient functional studies of this important plant.
