Welcome to PICKLES, the database of Pooled In vitro CRISPR Knockout Library Essentiality Screens, where end users can display and download raw or normalized essentiality profiles for more that 18,000 protein-coding genes across more than 50 cell lines. An additional data set with 15,000 genes targeted by pooled library shRNA in over 100 cell lines is also included. PICKLES allows expert and novice biologists the opportunity to see at a glance the relative fitness defect and tissue specificity of their genes of interest, generate and save figures locally, and download all raw data. Source
To search for a gene, type the HGNC alias for a specific gene in the white input box and press TAB or ENTER.
If the gene exists in the database, the corresponding graphs will be displayed (as shown below).
If the gene does not exist in the database, a message will be displayed (as shown below).
To view the specific value of the Essentiality Score, Normalized Bayes Factor, FPKM Expression, or CCLE Microarray Expression for a specific cell line, search for the cell line in the appropriate graph and hover the mouse cursor over the corresponding point. The information will then be displayed (as shown below).
Observable with 4/5 plots, is a Tissue Specificity P-Value. A Wilcoxon ranked test was performed for each tissue type across all genes. The lowest tissue P-Value accompanies each plot, suggesting that the displayed tissue has the largest mean difference compared to the rest of the group.
The tissue key illustrates the corresponding tissues of the cell lines in the x-axis. To see the corresponding cell line, hover over the tissue key. As seen below, the tissue key shows clusters of pancreatic tissues on the left side.
To filter tissues, have the desired tissues checkboxes selected and deselect any unwanted tissue checkboxes.
To hide a specific dataset in a graph, click on the corresponding colored rectangle under the "Click to remove" title.
To download a specific graph, click on the corresponding button below the graph. To download all the graphs, click on the button labeled "Download All Graphs."
IMPORTANT: Make sure that the browser window is open large enough that the width of the browser is greater than the width of the graph(s) that you are downloading. If not, the image of the graph(s) will be cut off whereever the width cuts off in the browser window.
The correct way to make sure the entire graph is downloaded is shown below on the right. Even though the entire height of the graph is not seen in the browser window, the entire width of the graph is seen in the window, ensuring that the entire height and width of the graph will be downloaded.
As shown below on the right, if the browser window is not at least the same width of the graph, when the graph is downloaded, the width of the graph will be cut off. However, even though the full height of the graph is not in the browser window, the full height of the graph will still be downloaded.
Fixed file download bugs and added links
Updated data query method and file size
Added Wilcoxon Rank-Sum Test of Tissue Specificity
Tissue Filtering Automatic Changes
Added Tissue Filtering
Added Gene Data Buttons + Functions
updated URLs for PICKLES.hart-org.lab
moved all data files to Data directory
Fixed download graph button so that selected gene name displays in image
Added content to contact page
Added content to home page
Added content to FAQs page
Fixed images on tutorial page
Adjusted size of headers and text
Added missing cell line to Wang screens
Fixed tissue keys so that a user can see the name of the cell line when hovering over the tissue key
Fixed issue on tissue key on GeCKO Screen Graph
Fixed download image page so that image gets downloaded with a specificed file name and extension
Removed sitemap page
Fixed formatting issue on tutorial page
Combined all the html files (representing different tabs) into one html file to prevent having to reload files each time the essentiality map tab was clicked
Added buttons to download the graphs in the essentiality map tab either separately or all together
Turned one page database into multipage database of multiple html files
Added content to pages
Changed the links on the files to make them automatically download instead of being directed to another URL
Fixed splicing issue in code so that graphs remain consistent
Loading page added to show when each data set has loaded (to account for slow load time)
Changed code to account for "nan" in data sets
|Screen||Data Type||Number of Genes||Number of Cell Lines|
|shRNA Essentiality Screens||Essentiality Score||13395||112|
|GeCKO Screens||Normalized Bayes Factor||15466||33|
|log(CCLE Microarray Exp)||18989||1038|
|TKOv1 Screens||Normalized Bayes Factor||17230||10|
|Tzelepis AML Screens||Normalized Bayes Factor||17997||5|
|Wang Screens||Normalized Bayes Factor||19161||19|
Click on the question to view the answer.
Raw read count data from all datasets was acquired and processed with BAGEL. BAGEL is a Bayesian classifier trained using gold standard reference sets of essential and nonessential genes. The observed fold changes of gRNA targeting uncharacterized genes are compared to the observed fold change distributions of gRNA targeting genes in the training sets and a log Bayes Factor (BF) is calculated. The BF represents the relative confidence that the gene is essential.
Fragments per kilobase of transcript per million mapped reads (FPKM) is a gene expression metric that is proportional to the observations of a fragment in a particular transcript. Source
mRNA expression profiles of genes across many cell lines. Not every cell line is currently found in CCLE, however in the future, we hope to incorporate more cell line expressional data in our maps. Source
Dashed threshold lines represent a low-stringency threshold for gene essentiality. Source
For optimal use of PICKLES please use Safari or Google Chrome. Firefox will not load all library plots. Additionally, please attempt to clear cookies from browser and consider a hard refresh to bypass cache (command+shift+r for MacOS and control+F5 for Windows). Source
Use this form to plot the normalized essentiality scores for your favorite gene. Please See FAQs for Map Loading Issues.
Plot Essentiality for this Gene (hit tab or enter to search):