The functional landscape of essential genes from pooled, image-based CRISPR screens

The data presented in this web portal are from pooled, image-based CRISPR knockout screens in HeLa cells. First, a fixed-cell primary screen targeted 5,072 fitness-conferring genes, with phenotypes measured using fluorescence microscopy of stains for DNA (DAPI), tubulin (antibody), gamma-H2AX (antibody), and actin (phalloidin). A secondary screen collected live-cell image phenotypes of cells expressing mCherry-tagged Histone H2B for 239 of these gene targets. See the “About” page for more about the screens and the data. Included in this portal are montages of individual interphase and mitotic cell images for each gene target from the fixed cell screen and time lapse montages of individual mitotic events for the genes included in the secondary screen. Also included are interactive tools for exploring a subset of the 1084 phenotypic parameters extracted from the primary screen images and the functional landscape of essential genes derived from high-dimensional analysis of these parameters. Enjoy!

How to navigate
  • To explore the numerical data, start by using the volcano plot (left) or PHATE landscape plot (right) below. For the volcano plot, select a parameter of interest to show the phenotype score for each gene knockout (x-axis) plotted against its corresponding statistical significance when compared to cells carrying non-targeting CRISPR sgRNAs (y-axis). For the landscape plot, select either the interphase or mitotic landscape to display how gene knockout phenotypes cluster together when the full range of extracted phenotype image parameters are accounted for. Hovering over individual data points on either plot displays the gene identity and its cluster membership below the plot. Click on a data point to navigate to a table of genes in the same cluster with links to individual gene information.
  • Click the "Compare" button to the left to explore combinations of individual phenotype parameters from the primary screen.
  • Use the box below to search for specific genes of interest, or click “Browse” to display a table of all gene targets which can be filtered or sorted for specific genes and parameters.
  • The individual gene pages contain montages of interphase & mitotic cell images from the screen as well as additional information about each knockout. See the bottom of this page for example genes to explore.



Interphase phenotypes
    large nuclei and increased 𝛾H2AX
    large nuclei and increased 𝛾H2AX
    multi-nucleated cells
    small nuclei
    small nuclei and cells
    increased tubulin and small cells
    increased tubulin
    decreased tubulin
    increased actin
    decreased actin


Mitotic phenotypes
    monopolar spindles
    chromosome alignment defects
    spindle defects


Live cell screen phenotypes
    long mitosis, chromosome alignment defects
    long mitosis, chromosome alignment defects
    long mitosis, chromosome alignment defects
    long mitosis, chromosome alignment defects
    long mitosis, chromosome alignment defects
    short mitosis