Additional file 8 of Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells

Additional file 8: Supplementary Table 4. Gene-Specific Analysis of Differential Expression in 27 h Tg(hmx CNEIII:cos:Gal4-VP16,UAS:EGFP)SU41-expressing V1 and dI2 Spinal Cord Interneurons Isolated From Uninjected Control and hmx2;hmx3a Double Morphant Embryos. Gene-Specific Analysis (GSA) was performed to analyze differential gene expression in V1 and dI2 spinal cord interneurons between 27 h uninjected control and hmx2;hmx3a double morphant samples (see Methods). Column A lists the gene symbol. Note that skor2, neff1, isl1a, pou2f2a, pou2f2b and zfhx3b genes returned previous gene names in the Lawson annotation. For ease of comparison, the current gene names shown in this paper are given in column A, with the Lawson gene symbols shown in parentheses. Column B provides the P-value for the comparison. This has not been corrected for multiple testing. Column C provides the P-value corrected for multiple testing by the application of the False Discovery Rate (FDR) Benjamini Hochberg method (46). Column D shows the ratio of the least squares mean reads for the antecedent (first population, column F) versus the consequent (second population, column G) population in the comparison. Column E shows the fold-change. The fold-change is converted from the ratio values in column D. When the ratio in column D is greater than 1, the fold-change in column E is identical to the ratio in column D. When the ratio in column D is less than 1, the fold-change in column E is calculated using the formula: -1/ratio. Each row corresponds to a distinct gene symbol. Each sheet has been sorted by the fold-change value in column E, from smallest to largest value. Consequently, negative fold-change values are shown at the top of the sheet, with positive fold-change values at the bottom of the sheet. Negative fold-change values occur when the least squares mean reads for the antecedent (first population in the comparison, column F) is less than the least squares mean reads for the consequent (second population in the comparison, column G), and so expression of that gene is upregulated in the consequent (second) population in the comparison. In contrast, positive fold-change values occur when the least squares mean reads for the antecedent (first population in the comparison, column F) is greater than the least squares mean reads for the consequent (second population in the comparison, column G), and so expression of that gene is upregulated in the antecedent (first) population in the comparison.