Fig 2: Genomic organization of SEPT9. The UCSC genome browser (http://genome.ucsc.edu) was used to display the location and genomic organization of SEPT9 on chromosome 17q25. (A) Genomic region covering approximately 300 kb: the eight amplicons (IDs given in red letters and within brackets) are shown after aligning their sequences using BLAST; CpG islands are shown in the track above the amplicons and gene transcripts are shown in the tracks below the amplicons. CGIs were numbered for easier reference within this manuscript. The UCSC display of transcripts is annotated with the combined IDs from Ensembl and NCBI/gene map for easier cross platform identification. (B) Detail of approximately 6 kb showing a higher resolution of the locations of the closely neighboring amplicons 4 to 7.

Fig 3: Bisulfite DNA sequencing results for SEPT9 amplicons. Each column displays results from one amplicon and each row displays results for one cell type. Within each of the rectangular boxes, the columns correspond to single CpGs and the three rows correspond to three patients. As all amplicons are drawn to the same scale the location of the amplicons is illustrated at the bottom with arrows pointing to the genomic map (compare to Figure 1). Color coding: yellow = unmethylated (0%), green = partially methylated (50%), blue = fully methylated (100%), and lighter or darker green/blue colors provide methylation levels below or above 50%. White areas = no sequencing data available. Abbreviations: str = stromal cells, epi = epithelial cells, Norm = normal colon tissue, NAT1 = normal adjacent tissue (1 cm away from tumor), NAT2 = normal adjacent tissue (> 10 cm from tumor), Adeno = adenoma tissue, pat = patient no.: only the last number of the patient ID in Additional file 1: Table S1 is shown here.

Fig 4: Box plot diagrams of SEPT9 methylation. Results from amplicons 4 and 5 in different LCM tissue specimens. Data are shown separately for stromal (str) and epithelial (epi) cells and for the three patients in each group. Red = epithelial cells, blue = stromal cells. The horizontal bar within boxes shows the median, dots within the boxes the means, the lower and upper boundaries of boxes show the 25th and 75th percentiles, the whiskers are determined by the 5th and 95th percentiles.