Sentence examples for lists were identified using from inspiring English sources
Similar gene lists were identified using the automatic hyper-geometric distribution tests in the Gene List inspector function of Gene Spring.
GO categories enriched in the L. major DE gene lists were identified using the GOseq package in R [ 101].
Genes significantly overrepresented in the target lists were identified using the statistics (hypergeometric distribution) implemented in the 'GO browser' of Spotfire DecisionSite for Functional Genomics.
Significant overlap between transcript lists was identified using hypergeometric tests.
Gene synonymies used in the literature searches of the candidate mouse genes are listed in Table 3. Putative Drosophila homologs of the mouse genes from the candidate gene list were identified using FlyBase [http://flybase.org/] [93], the Mouse Genome Database (MGD) [URL: http://www.informatics.jax.org; January, 2009] [108], and TreeFam [http://www.treefam.org/] [95], [96].
Gene ontology biological processes enriched in each gene list were identified using DAVID online tool [ 26].
All the previously reported seed protein and oil QTL listed in SoyBase were identified using linkage analysis and thus, the causal gene(s) could be located a substantial distance (in cM) from the markers which were reported to be genetically linked to the QTL.
Ontological categories overrepresented in lists of differentially expressed genes were identified using DAVID [ 19]; complete lists are given in Additional files 3, 4, 5, 6 and 7. To condense redundancies, we have also identified clusters for differentially expressed ontological categories in the sensitive vs. Erlotinib-, Irreversible- and Cetuximab-resistant groups (see below).
The list of DEGs that were identified using NOISeq (probability 0.8 as a threshold) is presented in Supplementary Table S6.
Lists of differentially expressed genes were identified using the statistical analysis of microarray algorithm [16] (SAM, Version 2.21, release date 2005-8-24; typical false discovery rate of 1% and 10%), and custom R scripts written in our laboratory.
Enriched GO terms within the lists of differentially expressed genes were identified using the GOEAST web server [ 53].
