Most of the information provided by this server are within the public domain and can be accessed via Web interface. The public domain information on the CSB.DB Web pages can be freely downloaded here and reproduced. Please contact the CSB.DB-Curator if you miss necessary information therein.
Below are the list a frequently asked questions.
Where can I find help?
Currently Help information can be accessed by pressing on the information button (i) or by pressing on the detailed information button (iD). If you think you found an error or a missing feature contact us...more help
What is it all good for?
CSB.DB is meant to help finding transcripts/metabolites/proteins etc. which are co-regulated with other transcripts/metabolites/proteins. Just assume you identified two downstream target genes of your favourite transcription factor. Then if you are lucky they would be co-regulated and now you could ask the question, which other genes are also co-regulated and might thus also be target genes. That is where CSB.DB comes in. In this case an intersection gene query would be what you wanted.
Which browsers are supported?
I can not see all pictures. What should I do?
For various HTML pages we use png instead of gif files. Not all browser (especially older) support the png files. Update your browser to get the newest stable version, e.g. for Microsoft see windowsupdate.microsoft.com.
Why can't I download the results from the queries?
Please use our text exporter on the top of the query result pages. The downloaded file is zipped. Unzip with WinZip or other software and you can upload the text file in MS Excel or in a text editor. The results are tab delimited.
Why does the network visualization not work?
Make sure you have java version 1.4 or better installed (java download) and make sure you enabled java support for the internet. You can test it (incl. version) on Sun's Test Java Virtual Machine web page.
What is the network visualization good for?
If you want to figure out, if some of your genes cluster together or if special genes form 'hubs' in a response network. If the latter is the case they might represent important regulation points.
Why is there no info for my gene, I found it on the Affy chips?
Due to the generation of the correlation matrix which discards data spots not well measured, it happens that whole transcript spots are not available. Just imagine the following situation: Six microarray experiments, where in the first three you measure YFG1 but for YFG2 you only get absent calls. In the next three you can measure YFG2 but get absent calls for YFG1. Since correlation is based on genes being CO-regulated no correlation between those two could be measured.
What is this Spearman / Kendall / Pearson?
These are correlation coefficients which measure how strongly transcripts/metabolites etc. are co-regulated over experiments. They are a measure how much alike the behaviour is over the experiments, e.g. do they go up and down together. In general Pearson is parametric and the other two are non-parametric making them more robust to individual outliers...more
Where do I find a scatter plot?
After querying for your gene click the links on the correlation coefficients between your gene and a second gene. A new page will open, where you can amongst others choose scatter plot.
How do I get the values into MS Excel, OO/SO etc?
Mark the whole table press Ctrl-C (Apple-C) in your spreadsheet application press Ctrl-V (Apple-V).
Where do these Arabidopsis annotations come from, I quite like them?
They were assembled by Oliver Thimm at the Max Planck Institute of Molecular Plant Physiology (MapMan; Thimm et al., 2004). The annotations are currently revised.
Where can I see expression data for my gene?
An obvious resource would be the Stanford Microarray Database (SMD). CSB.DB only incorporates correlation between transcripts/metabolites etc but not the raw values.