Additional file 10.

Table S6. Gene expression analyses of the P. profundum SS9 genes. Column (A): starting from origin of duplication, genes are numbered according to the position on the genome and on chromosomes; column (B): locus tag; column (C): Swiss-prot ID; column (D): gene name; column (E): gene description downloaded from NCBI database; column (F): gene description obtained from CMR (Comprehensive Microbial Resource) (http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi); columns (G-H: COG code and COD ID; columns (I, J, K, L): chromosome, strand, start and stop position of the genes; columns (M, N, O, P): number of reads mapped on genes in the four experiments (DB110 at 28 MPa, DB110 at 0.1 MPa, TW30 at 28 MPa and TW30 at 0.1 MPa. All values are normalized considering the total number of reads mapped on the reference sample (DB110 at 28 MPa); columns (Q, R, S, T): reads per kb per 1 million reads mapped (RPKM) values are reported for the same four samples (DB110 at 28 MPa, DB110 at 0.1 MPa, TW30 at 28 MPa, TW30 at 0.1 MPa); columns (U, V): log2 ratios and p-values calculated using DEGseq software for the comparison between DB110 0.1 MPa and DB110 28 MPa; columns (W, X): log2 ratios and p-values calculated using DEGseq software for the comparison between TW30 28 MPa and DB110 28 MPa; columns (Y, Z): log2 ratios and p-values calculated using DEGseq software for the comparison between TW30 0.1 MPa and DB110 0.1 MPa; columns (AA, AB): log2 ratios and p-values calculated using DEGseq software for the comparison between TW30 0.1 MPa and TW30 28 MPa; columns (AC, AD): log2 ratios and p-values calculated using DEGseq software for the comparison between TW30 0.1 MPa and DB110 28 MPa; column (AE): gene ID of the orthologous V. cholerae genes belonging to the ToxR regulon; column (AF): gene name; column (AG): gene function; column (AH): gene description; column (AI): gene ID; column (AJ): log2 ratio of gene expression values determined in V. cholerae toxRS mutant compared to N16961 strain; column (AK): log2 ratio of gene expression values determined in V. cholerae tcpPH mutant compared to N16961 strain; column (AL): log2 ratio of gene expression values determined in V. cholerae toxT mutant compared to N16961 strains.

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Campanaro et al. BMC Genomics 2012 13:567   doi:10.1186/1471-2164-13-567