Frequently Asked Questions

1. What data is available?

The core data consists of processed gRNA counts across diverse tissues, with the raw sequencing data and the analysis code additionally available for iMAP-100.

Links to all available data (processed, raw, and code) can be found on the Downloads page.

2. iMAP-100 and iMAP-91 carry 100 and 91 guides, respectively. However, the heatmaps display only 98 and 87. Why?

The first and last guides in the iMAP transgenes were designed for characterizing recombination, and thus deleted from the heatmaps for clarity. For iMAP-91, two additional guides were deleted: a duplicate of a non-targeting control (made by mistake) and a guide targeting Ptprc/Cd45, the former designed by mistake and the latter irrelevant to RNA modifications.

3. How do I use the network graph?

The network graph visualizes the relationships between different guides in the perturbation datasets. Nodes represent guides, and the edges (lines) between them represent calculated interactions or similarities based on the experimental results. Explore the graph to uncover patterns and connections within the perturbation data.

Navigate: zoom in and out using mouse wheel or trackpad. Click and drag the background to pan across the network.
Identify the connections to a gene of interest: To this end, enter the node of interest (NOI) and select the node from the pop up menu. This will bring up the network of genes surrouding NOI, including the genes directly connected to NOI. Besides, double-clicking on any node within the network can display the connections to that particular node. Click the blank background to cancel.
Display details: Single-click on a node (guide) or an edge (interaction) to display detailed information.
Filtering: Use the control panel (near the graph or accessible via a button) to filter the displayed nodes. For example, set the '# Impacted Tissues' slider to show only guides affecting a small number of tissues, and adjust the 'Fold Change' slider to show only those with a high effect size (e.g., Log2 Fold Change > 1, which corresponds to a fold change > 2). Click 'Apply Filters' to update the view. Use 'Reset Filters' to return to the default view.

4. How can I cite iMAP?

Please cite our database according to the dataset you used:

For iMAP-100 dataset, please cite:
Liu, B. et al. (2022) 'Large-scale multiplexed mosaic CRISPR perturbation in the whole organism', Cell, 185(16), pp. 3008-3024.e16.
For iMAP-91 dataset, please cite:
[Citation information will be added]

5. Why do some volcano plots show many points aligned horizontally at the top?

Points with a p-value of 0 cannot be plotted directly on a logarithmic scale (-log10(0) is undefined).

For visualization purposes, these points are displayed at a position corresponding to p = 1e-10 (or a similar small value) on the volcano plot's y-axis (-log10(p-value)). This allows them to be visualized without distorting the scale for other points.

However, the original p-value (0) is preserved and correctly shown when you hover over the point or look at the data in the results table below the plot.