M.Parisi, R.Nuttall, D.Naiman, G.Bouffard, J.Malley, J.Andrews, S.Eastman, B.Oliver, Paucity of genes on the Drosophila X chromosome showing male-biased expression, (Science 299: 697-700; 2003).
The Parisi et al. (2003, 2004) experiments used arrays of approx. 14,000 PCR amplicons. The amplified probes (average length 450 bp) corresponded to predicted exons of all genes in D. melanogaster genome release 1.0. The array platform is described under GEO Platform GPL20 and the individual hybridization results are available under GEO accessions GSM2456, GSM2457, GSM2458, GSM2459, GSM2460, GSM2461, GSM2462, GSM2463, GSM2464, GSM2465, GSM2466, GSM2467.
The first 4 of the above accessions are for whole males vs. whole females, the next 4 are for gonadectomized males vs. gonadectomized females, and the final 4 are for testes vs. ovaries. In all cases 4 replicate hybridizations were performed, including biological and dye-swap replicates. All hybridizations used 5-7 day old flies of the y1w67c strain.
In Sebida, the testes/ovaries ratios given by the authors in the supplementary data to their 2003 paper are provided. In addition, we also calculated average ratios over all hybridizations listed as GEO accessions above and provide these as Parisi (2004) data. There may be slight differences between the testes/ovaries ratio from 2003 and that of 2004, even though they are based on the same data. This is due to slight differences in the way the averages were calculated and the fact that Parisi et al. (2003) only considered probes for which a good signal was available in all replicates. For the 2004 calculations, probes without signal were treated as missing data. P-values were calculated from the raw data given in the GEO accessions using a Bayesian method (BAGEL) developed by Jeffrey Townsend.
In cases where there was more then one probe per gene, we used the average over all probes. Note that the ratios presented in Sebida are straight ratios and not ln or log2 transformations.