PathON - Pathway Analysis Tool
The goal of the fly synexpress tool is to allow researchers to compare and visualize transcriptomics data. In particular, we aim to support visualization of data for more than one gene, such as genes identified as related using an orthologous approach. The underlying data used at fly synexpress are data available from a number of public sources, including the modENCODE project. Ultimately, the results from a fly synexpress search might help in development of testable new hypotheses.
If you are starting with a single gene, you can enter the gene and click to view in what cells, stages or tissues, or under what conditions, evidence supports the idea that the gene is expressed.
If you are starting with a list of genes (the primary use we expect for fly synexpress), you can enter the gene list (in the text box or uploaded as a list) and similarly view in what cells, stages or tissues, or under what conditions, evidence supports the idea that those genes are expressed.
We have also provided some pre-defined lists, such as kinases. Similar to a custom gene list search, you can select one of these lists, select in cells, stages or tissues of interest, and view a heatmap of expression.
Initial results a bit overwhelming? We suggest limiting your results by selecting specific sub-categories withing cells, stages, tissues or conditions, in order to refine your search.
Want to show the heatmap at a lab meeting or include it in a publication? You can [how would they save? click to download?] the file or insertion into a poster, slide talk or publication. Please cite the fly express URL and associated publication [we'll link to the publication when there is one] when you show a heatmap or otherwise use results obtained here.
Is this the final word on Drosophila gene expression or pre-defined gene lists? Not a chance. New expression data are made available all the time. Any given data point would need to be validated. Expression of a gene in cells that comprise only a small portion of a tissue can be masked by what's happening in more abundant cells. No one expert would fully agree on a complete and final list of even something as well-defined as kinases. You should have these caveats and more in mind as you use fly synexpress or other similar resources.
For precacluated input files, the format is a two column file: [gene, log2ratio]for hitlist analysis no ratio is required, the file is simply a list of genes, one per line or row.
Calculation of Ratios
the PATHpt tool can calculate the log2 Ratio from your raw data. To do so submit an excel file with the columns header as the first line. The header must contain the following names
- gene :the fbgn or gene name
- control the control values (one or more columns)
- data the data values (one or more columns)
for csv files tab seperated is prefered, but comma separated should work. See exmple files.