This website is designed to explore genomic and transcriptomic dataset from plant. We have collected publicly available microarray and RNASeq datasets to perform Boolean analysis on Arabidopsis thaliana.

How to cite

Pandey, S, Sahoo, D. Identification of gene expression logical invariants in Arabidopsis. Plant Direct. 2019; 3: 1– 9. https://doi.org/10.1002/pld3.123

Tutorial

The Home link above will take you to the home page where there are links to two different tools to explore Arabidopsis thaliana datasets.

The About link above will take you to this page again.

The Contacts link above will take you to a page with information about the authors and contributors.

In the Home page there are links to following two different tools:

HEGEMON scatterplot explorer links are identified by the following links in the Home page:

HEGEMON annotation browser links are identified by "Plant microarray annotation browser (Click here to get access)" under the heading "Annotation Browser".

HEGEMON scatterplot explorer

When you click the "Explore" link you will see a page like below:

  1. Select Dataset: select a dataset to analyze by using the dropdown menu.
  2. topGenes: This button click lists top nG (you can enter a number in the textbox) differentially expressed genes (default 10).
  3. Gene A: Type a gene name in the textbox (Gene Symbol Name, Affymetrix ID or AGI code AT#G#####). Gene A is used in the X-axis of the scatterplot.
  4. Gene B: Type another gene name in the textbox (Gene Symbol Name, Affymetrix ID or AGI code AT#G#####). Gene B is used in the Y-axis of the scatterplot.
  5. getIDs: Lists the probe IDs present in the selected dataset. Click on this button to make sure that a probe exists in the dataset.
  6. getPlots: Shows scatterplots with all combinations of the probe IDs between gene A and gene B. At this page the users can select their favorite scatterplots by clicking mouse in the middle of the scatterplot. Once a scatterplot is selected textboxes corresponding to Gene A and Gene B are changed to reflect the selection.
  7. getStats: Shows scatterplots and various statistics with all combinations of the probe IDs between gene A and gene B. For each scatterplot a statistical test was performed to check if there is a Boolean implication relationship between Gene A and B. At this page the users can select their favorite scatterplots by clicking mouse in the middle of the scatterplot. Once a scatterplot is selected textboxes corresponding to Gene A and Gene B are changed to reflect the selection similar to getPlots.
  8. Explore: Shows the selected scatterplot with a new set of tools on the right.
    1. Selecting samples using Mouse
    2. Highlighting the samples using the checkbox on the left side of "Group 0".
    3. Highlighting multiple groups using the checkbox on the left side of "Group 0", "Group 1", "Group 2".
    4. Extracting the GEO links to the experiments: Select the checkbox on the left of "Group 0" and click on the button "Show" above.
    5. Selecting Tissue Annotation: Click on the drop down menu "Select Patient Information" and select "c Tissue".
    6. Selecting Root Samples: Click on the drop down menu "root" after selecting Tissue annotation above.
    7. Selecting Flower Samples: Click on the drop down menu "flower" after selecting root samples above.
    8. Highlighting Root and Flower Samples: You can change the names of the respective groups "Group 0" to "Root" and "Group 1" to "Flower". Click on the checkbox to highlight them in the scatterplot.
    9. Boxplot of Root and Flower Samples: After selecting the checkbox on the left side of "Root" and "Flower" click on the button "BoxP" above.
    10. Download scatterplots, boxplots and results of different statistical tests: After selecting the checkbox on the left side of "Root" and "Flower" click on the button "Download" above. It opens a new page with a pdf file: Hegemon-plots .

HEGEMON Annotation browser

Comming Soon!! Please check back later.

Software

https://github.com/sahoo00/BooleanNet

https://github.com/sahoo00/Hegemon

Data

GSE118579 - Identification of gene expression logical invariants in Arabidopsis

Acknowledgement

Dr. Debashis Sahoo is supported by startup funds from the Department of Pediatrics at University of California San Diego, and a R00 grant from National Institute of Health, USA (R00CA151673).