Diel Explorer

This tool is brought to you by the Gehan Lab at the Donald Danforth Plant Science Center. For the code used to generate this app, please visit our Github . For more information on how the data was processed please refer to doi: https://doi.org/10.1101/131185 . To download the raw data go here:

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.

Sample Info

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




Browse and Filter Data

Plot Data

We restrict plotting to 100 genes. Please download data from 'Search and Browse Data' tab or run a local installation of Diel Explorer if you want to graph more genes.

Download Line Graph Download Heatmap

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.

Contact US

For questions or if you are interested in adding your own data contact Malia Gehan

For mor information on the Gehan lab visit our website