Select cluster gene set

3D-Cardiomics allows you to view the adult heart transcriptome in 3D, compare pieces of the heart, and view similarly expressed genes! Please refer to the quick start guide below for more information.

Created by Monika Mohenska*, Nathalia M. Tan*, Alex Tokolyi*, Milena B. Furtado, Mauro W. Costa, Andrew J. Perry, Jessica Hatwell-Humble, Jan M. Ruijter, Hieu T. Nim, Susan K. Nilsson, Nadia A. Rosenthal, David R. Powell, Fernando J. Rossello, Mirana Ramialison^, and Jose M. Polo^.

Please visit our GitHub repository to access the source code for 3D-Cardiomics.

Quick Start Guide

1. Searching for a gene

We use the MGI gene symbols (GRCm38, MGI vM9). To find the one which is synonymous with your target gene, please perform a query here: http://www.informatics.jax.org/batch

Once you have the MGI gene name, enter it in to the search field at the top of the screen, then select your target gene to load it on to the 3D heart.

2. Adjusting the view

If you want to view inside the heart, click the ‘Expand’ button to spread out the pieces, and click it again (or press the ‘Reset’ button at any stage) to return it to normal. To rotate the heart, you can click and drag with your mouse or use the directional keys on your keyboard.

A key which explains the relative highs and lows of the gradients can be found by hovering the mouse over the colour symbol in the top left corner. To switch between absolute mode (A), and normalised mode (N), click on the (A) symbol. On top of this, clicking the eye symbol enables colour blind mode, using a narrower range of colours but ultimately representing the same information.

3. Viewing similar genes

After selecting a gene from the top menu, similar genes (by Pearson correlation) will be calculated and the coefficient of determination (as a percentage) presented in the panel on the right side of the screen. Clicking any of the names will load the gene on to the 3D heart.

4. Comparing expression between heart pieces

Begin by selecting the red ‘Compare’ button on the panel on the left side of the screen. The indicator will then change to ‘Select Group 1 Piece(s)’; click on the heart pieces to add them to the first group, and click again to remove them. Selected heart pieces will be outlined in blue.

Reclick the red left button as it now changes to ‘Select Group 2 Piece(s)’. From here you can again click pieces to add to the second group, or click the orange complement button on the left to select all remaining pieces.

Clicking the red button will begin the computation, this should take at most 10 seconds. The resulting table will list the gene name (which you can click to load the gene on to the 3D heart), the fold change between the two groups, and the false discovery rate (FDR). Click the blue button to toggle between sorting by the log fold change (FC) and the false discovery rate (FDR).

5. Viewing the average expression of a gene set

Gene sets can be uploaded to view the average expression for those genes (eg for genes from a particular pathway). Click the 'Upload gene set' button and select a file containing a list of genes in the file selection popup. The gene list must be a text file with one gene symbol per line. Gene sets in 'grp', 'text' and 'gmx' formats from MSigDB also work, as long as all gene names are valid MGI gene symbols.