Interestingly, three out of four pairs from Germany and a published French draft genome of a C. ulcerans isolate cluster together, as also depicted by the phylogenetic analysis using the genome-wide data.
All URLs for the analysis programs are listed in Additional file 2. Genomic DNA (~600 ng) from each sample was processed with SNP chip analysis using the Genome-wide Human SNP Array 6.0 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's instructions (Additional file 1: Table S1).
In our study, nine ZmNAS genes were systematically identified and characterized through genome wide analysis using the current version of maize inbred line B73 genome database.
Datasets were selected on the following criteria; analysis of primary human tumour samples, large study size, availability of raw data with provision of clinical annotation and genome-wide analysis using the Affymetrix U133 platforms (either U133A + B or U133Plus2.0).
In this study, our genome-wide analysis, using the recently closed genome sequence of E. amylovora Ea273 identified a total of 46 TCST genes in E. amylovora including 17 sensor kinases, 20 response regulators, three hybrid HKs, four RRs with enzymatic output domain (EAL-GGDEF proteins), and two kinases.
The program PLINK [40] was used for the genome-wide association analysis using the v2 platinum SNP set with minor allele frequencies >0.05, 75% genotype calls and no more than 25% missing genotypes per individual.
The DNA extraction protocol is described in Additional file 1. Genome-wide methylation analysis using the Illumina Infinium Methylation27K beadchip (Illumina Inc., USA, WG-311-1201) was performed.
We assayed 149 tumors from 149 patients, 53 Ta, 45 T1 and 51 MI tumors, for genome-wide methylation analysis using the Illumina Infinium HumanMethylation27K BeadChip.
The genome-wide linkage analysis using the interval mapping method, assuming a binary trait on 55 F2 progeny, yielded a LOD score peak on mouse chromosome four flanked by the markers D4Mit108 and D4Mit139 with a LOD score (LOD = 3.8) exceeding the threshold level for significance at 95% confidence (Fig. 4B).
In a genome-wide expression analysis using the NimbleGen microarray platform, of Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) in Populus (Populus trichocarpa clone Nisqually-1), the genes in a subgroup of Aux/IAA showed differential expression among different tissue types [ 18].
