Using this Tool
In the SAMPLE INFO tab see the available datasets and conditions
In the SEARCH AND BROWSE DATA tab above, you can search for genes of interest using by either the search bar or by uploading a .txt file with gene ids. Alternatively, you can use the data filters to browse the data.Once you have loaded or searched for your selections the data can be viewed and dowloaded. A plot of the data can be seen on the Plot Data tab once the plot button is hit. Warning: asking to plot a large line graph is messy, we would suggest switching to a heatmap
In the PLOT DATA tab above, data selected from Select Data or Browse Data tabs is plotted
In the ADDING YOUR OWN DATA tab above, we briefly describe how to alter this Shiny App so you can graph your own timecourse data.
Notes for Reference XXX: Setaria viridis was grown for 10 days then released into constant conditions for circadian sampling every 2 hours for 48 hours. Again, for more details sampling conditions, please refer to XXXXX(Pub/Preprint). The two entrainment conditions for this experimental set are as follows:
Search Data with GENEID or GO
Search using small sets of GENEIDs
GENEIDs, Orthologs, or GO separated by a comma are allowed
Search using small sets of GO TERMS
Search using small sets of ORTHOLOG GENEIDs
refresh page to clear search
Search Data with File
Upload a file of GENEIDs, the GENEIDs should not be quoted, one line per geneid
Upload a file of ORTHOLOG GENEIDs, the ORTHOLOG GENEIDs should not be quoted, one line per geneid
refresh page to clear search
Genes, Orthologs, or GO Selected with Search
Adding Your Own Data
We encourage you to use this frame work to explore your own data and hope that you will add it to the public repository as well. If you have any problems adding your own data or with the exisiting data, please contact us . The following are the basic steps to add data.
STEP 1:Data Format
This takes in the resulting output of JTK Cycle . For more information on the parameters used to process data with JTK Cycle, please refer to XXX (preprint/pub). The resulting .txt files are then further processed in Step 2.
STEP2: Add Data and Format Further
Your sampling frequencing and headers may differ from ours. So you can alter your naming scheme to match ours, (if it makes sense to) or you might need to replace your data with ours. Replacing our data with yours is a bit more involved, because, it will change the header names for the graphing steps downstream. For now we will assume that your data headers are like ours. There is a R script in the data folder called setaria-circadian.R. The setaria-circadian.R script was used to add some additional information to the JTK Cycle output. For example, two JTK Cycle outputs were joined together with an rbind step then merged with an annotation file. We add in columns for species name, categories for BH.Q and ADJ.P, and then find the maximum expression value per replicate so that normalized data can be calculated. Once all of these things are done, we have have the raw (expression values not normalized to maximum) and relative/normalized expression data tables that are used as input data. Once you add the necessary columns your dataset, you could rbind it to to the Setaria dataset and reload the app.
STEP3: Add Sample Info
There is a file called entrainment.information.txt. Add a row to that file with your sample information and save it.