The following topics are covered below:
	Searching the Sebida database
	Individual gene pages in Sebida
	Downloading Sebida data
	Sebida analysis pages
	Sebida data and references
	Citing Sebida
	Contacting Sebida or submitting data
	Searching the Sebida database
	Perhaps the most useful function in Sebida is the search function. This can be used when you want to find the sex-bias information for a particular gene in one of the species contained within Sebida. For example, if you are interested in the Drosophila melanogaster ocnus gene, you can go to the search page and type 'ocnus' into the search field. The species can be selected by clicking the appropriate button below the search field. The default is D. melanogaster. Click the 'search' button to start the search.
	It is also possible to search by gene symbol or annotation number. For the above gene, these are 'ocn' and 'CG7929', respectively. The same terms can be used to search for D. simulans genes. For Anopheles gambiae, genes can be searched by Affymetrix probe ID or Ensemble annotation number. Further examples are provided on the search page.
	Individual gene pages in Sebida
	After a successful search, you will be taken to the Sebida report page for the appropriate gene. On this page you will find information about the gene, including the male/female (M/F) expression ratio from one or more experiments. The M/F is given as a straight ratio (not on a log or log2 scale). For Drosophila melanogaster, which has been used in many experiments, there is typically a long list of information. This includes the gene identification information (with a link to the FlyBase entry) and the results of the sex-bias meta-analysis.
	In the above example, the gene was classified as male-biased in the meta-analysis, with a M/F ratio of 18.6708. This means that the gene has over 18 times higher expression in males than in females. The difference in expression between the sexes is highly significant, with a p-value of zero (in Sebida p-values below 0.0001 are given as 0). The false discovery rate is less than one percent (FDR=0.03%) , meaning that of all the genes classified as sex-biased within this FDR group, less than 1% are expected to be false positives. In other words, we can be very confident that this gene really is male-biased. Below the meta-analysis results you will find the M/F expression ratios from the individual experiments and, when available, a link to the FlyAtlas tissue-specific expression entry for the gene. After the expression information, there is also information about recombination rate, codon bias, and interspecific divergence for the gene.
	Downloading Sebida data
	The data contained in Sebida can be downloaded from the 'download' page. Here there is an option to download all of the data for each species as a single text file. The files can be downloaded by right-clicking (or control-clicking on a mac) on the link and choosing 'Save link as ...'. The file will be saved as a tab-delimited text file that can be opened with Excel or other spreadsheet/text-editing software. Sometimes there can be problems with the number format (e.g., whether a period or a comma is used to denote the decimal place). If you have a problem with this, you can first open the text file with a text-editing program, do a search-and-replace (e.g., replace all '.' with ',' or vice versa), save the file, and then open the new version as a spreadsheet. For Drosophila melanogaster, the latest meta-analysis results are included in the 'Sebida_3.0' spreadsheet which was generated in July 2011. The older version 'Sebida_2.0' can also be downloaded. You can use the columns 'MetaClass', 'MetaM/F', 'MetaP', and 'MetaFDR' to sort genes by sex-bias classification, male/female expression ratio, p-value, or FDR, respectively. More information on the meta-analysis can be found on the classification page.
	Sebida analysis pages
	In the analysis section of Sebida, you will find the results of several analyses of sex-biased genes, including: the X:autosome distribution of sex-biased genes, rates of evolution of sex-biased genes, codon bias in sex-biased genes, and more. The analysis section is intended to be browsed and provides examples (with figures) of how Sebida data can be used for evolutionary analyses.
	Sebida data and references
	The original sources of all Sebida data (with citations) are provided on the references page. Here you will also find more detailed information about the statistical analysis and the molecular evolutionary analyses. Whenever possible, we have provided links to the original publications, datasets, or GEO/ArrayExpress entrees. There is also a section of additional references related to sex-biased gene evolution.
	Citing Sebida
	If you use Sebida for your published research, please cite the following: F.Gnad, J.Parsch, Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression, (Bioinformatics 22: 2577-2579; 2006).
	Contacting Sebida or submitting data
	Sebida welcomes submissions of original data regarding sex-biased gene expression. If you would like to submit data or have any questions or comments, please see the contact page.