Additional data file 1:

In the 'Statistics and annotation' worksheet, basic annotation data are given for each differentially expressed probeset, with the Affymetrix ID number, the gene symbol, chromosome number and starting/ending location, cytogenetic band, gene ontology/molecular function and the Affymetrix target description. Means and gene expression values are given on the transformed scale. The worksheet also contains information on the significance level of analysis of variance tests. The tests were conducted on the transformed gene expression values for each probeset separately. The p value for significant differences between conditions is listed if the parent p value is less than 0.05. Only genes that showed a significant difference between all the means on this scale, using a threshold of p ≤ 0.005, are included in the worksheet. 'Within B10' tests for differences within the B10^k conditions only (using only B10^k condition variance data), with subtests 'Within pre' comparing the B10^k pre-selection population sorted from insHEL transgenic and non-HEL transgenic hosts, 'PreS vs S-' comparing B10^k pre-selection populations to B10^k negative selection populations, 'PreS vs S+' comparing B10^k pre-selection populations to B10^k positive selection populations, and 'S+ vs S-' comparing B10^k positive selection populations to B10^k negative selection populations. 'Within NOD' tests for differences within the NOD^k conditions only (using only NOD^k condition variance data), with subtests performed as per the B10^k tests. 'Overall sig' tests for differences between any conditions, with subtests comparing B10^k versus NOD^k populations at the pre-selection stage ('PreS'), during negative selection ('S-') and during positive selection ('S+'). For each probeset the average expression is given as log₂ scaled and normalized and arithmetic normalized data, for each condition. Individual data for arithmetic normalized expression are also given for each replicate (PreS 1, 2 and 3 come from non-HEL transgenic hosts, 4, 5 and 6 come from insHEL transgenic hosts). Individual Affymetrix 'Present/Moderate/Absent' calls are given for each replicate. In the 'Raw data' worksheet the individual data for arithmetic normalized expression are given for each probeset, regardless of statistical analysis, along with the Affymetrix target description

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Additional data file 2:

The 'B10' worksheet contains information on the expression profiles (patterns) for all probesets that showed a significant difference between the means on the transformed scale, using a threshold of p < 0.05 for the B10^k strain. Along with the Affymetrix ID are listed the gene symbol, the pattern to which the probeset is assigned in the B10^k strain, the pattern to which the probeset is assigned in the NOD^k strain, the average arithmetic (unlogged) Affymetrix MAS 5.0 signal values for each condition in the B10^k and NOD^k strains of pre-selection ('PreS'), positive selection ('S+') and negative selection ('S-'), and the annotated molecular function. In the 'NOD' worksheet, all probesets that meet the significant cut-off for assignment to an expression pattern in the NOD^k strain are listed, in the same manner as the 'B10' worksheet. In the 'B10 vs NOD' worksheet, all probesets that meet the significant cut-off for assignment to a differential expression group between the B10^k and NOD^k strains are listed. Along with Affymetrix ID and gene symbol are listed the group number, the fold-change between the relevant B10^k and NOD^k conditions (dependent on differential expression group), the p values for differential expression between B10^k and NOD^k strains for each condition, the average arithmetic normalized expression for each condition in the B10^k and NOD^k strains, and the annotated molecular function

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