Guidelines for interpreting modENCODE tiling array expression data.

Each exon score is the median value for fluorescence from all tiling array probes that are contained within the coordinates of the annotated exon; each gene score is the maximum score for all exons associated with that gene. The units are arbitrary.

Exons are numbered from the 5' end of the gene to the 3' end; these exon numbers do not necessarily correspond to FlyBase exon identifiers. To find differences in expression of alternative transcripts, first view the annotated transcript models for the gene by clicking on the gene name or identifier at the top of the results page; this will take you to the corresponding FlyBase gene page. Using the exon coordinates, identify the exons of interest. You can then compare the ratios of their expression scores among the cell lines.

Because of sequence-dependent variations in the efficiency of hybridization to the probes on the array, it is NOT appropriate to compare scores for different genes or for different exons within a gene (e.g., do not try to interpret differences within a row). These scores are meant to be used for comparing expression of a given gene or a given exon or a ratio of two exons among cell lines (i.e. differences within a column are meaningful).

The range of scores is 0 to 53,808. Scores below 500 may be unreliable.

FlyBase annotation 5.12 was used in this analysis. If you have difficulty retrieving data for a particular gene, try synonyms listed in FlyBase, since later annotations have changed the names and/or identifiers for some genes.

For more information about modENCODE, visit the modENCODE site.