These were removed from predictions using the Tables function of the UCSC genome browser (http://genome.ucsc.edu).ucsc.edu
Exon coordinates were extracted from UCSC using the table browser function using the following tables: hg19: knownGenes; panTro3: refGene; mm9: knownGenes; danRer7: refGene; ci2: refGene; ce10: refGene; anoGam1: refGene; dm3: refGene.
Traits of gene presence/absence were plotted alongside the tips (see fig. 3) using the "table.phylo4d" function of the Adephylo package (Jombart and Dray 2010).
Mapping of DMRs to Refseq, CpG island, promoter, miRNA and small nucleolar RNA (snoRNA) was performed using the Table Browser function embedded in UCSC Genome Bioinformatics (Santa Cruz, CA, USA; http://genome.ucsc.edu/cgi-bin/hgTables?command=start) or by our customised web-based tool TileMapper (http://tilemapper.nichd.nih.gov/tilemapper) designed specifically for transfrag mapping.
Using the RAND ("TABLE",) function of SAS® 9.3, we specified the frequency with which each genotype appeared in each simulated population, assuming that hosts randomly sampled rhizobia and therefore the observed frequencies of the 22 NifD genotypes in the total sample of 81 nodules represented their availability in the Bradyrhizobium population.
Source: Mosaic Japan website; http://www.awkk.co.jp/mosaic/ We correlated the number of influenza patients and 5-year age group populations to the Mosaic Japan dataset using the Join Table function in ArcGIS Desktop 9.2, and then the total number of cases from each census enumeration district was aggregated by Mosaic Group and Type.
As the weight assigned to the two attributes is 0.1 (see Table 1: Weight reference table), therefore using the utility function, the initial DPV of Node A for each of the base stations is 0.2.
The stereo GMM is used to compute the CDF tables using the sigmoid function.
The significance level of differences in genotype frequencies between cases and controls per SNP was determined with a χ-test from 2 × 3 (genotypic) tables using the ccfast function in the GenABEL package in R [ 23].
To extract a table of the top-ranked genes from the linear model fit, we used top Table function from LIMMA.
