Our TranscriptomeViewer displays Affymetrix tiling chips and Illumina sequencing data for any queried gene. Each picture shows the queried gene plus 5 kb of flanking sequences on each side.

The plotted data are:

• Top panel (Tiling chip): the normalised data smoothed with a 5 probes sliding window (log2). Non-unique probes have been discarded (white gaps in the plots).
• Bottom panel (Illumina sequencing): the log2 of “sequence scores”. These are the number of time a given base is hit by sequence reads normalised for sequencing depth. Normalised scores equal to zero (no hit) have been given an arbitrary log2 score of -31 (for plotting purposes). Reads aligning to more than one genomic location have been kept in this dataset. Repeated regions (LTR, transposons, etc) may therefore receive disproportionately large numbers of hits.

Data for several conditions are available and can be displayed in two different ways:

• The Heatmap view (select “all” in menu) displays all conditions together along the genome annotation. Each line is a condition (see legend on left of figure). For the tiling chip data, the top and bottom strands are plotted above and below the genomic annotation, respectively. For the sequencing data, only one plot is available because this technique does not provide strand-specific data. The normalised signals or sequence scores are represented by a panel of 9 colours going from yellow (low) to brown (high).The red lines demark the start and end of the queried transcript in GeneDB.
• The Dots view (select any specific condition from menu) displays data for a chosen condition along the genome annotation. For the tiling chip data, the top and bottom strands are plotted above and below the genomic annotation, respectively. For the sequencing data, only one plot is available because this technique does not provide strand-specific data. The vertical lines in the tiling chip data represent “break points” determined during our analysis (R/Bioconductor package “tilingArray”, function “segment”). These break points have been used to determine automatically the UTR boundaries of all genes ). The red lines demark the start and end of the queried transcript in GeneDB.