The Gene Finder tool allows you to find a set of genes that meet multiple custom criteria.
Specifying criteria
Specify criteria in the "Build filtering criteria" panel that appears when you first access the Gene Finder.
Two major types of criteria may be specified:
- Lipid droplet criteria
- MAGMA parameters
If multiple criteria are selected, the list of genes returned will be those that answer all selected criteria.
1. Lipid droplet criteria
Genes may be filtered by one or more of 7 criteria.
Determinant of LD morphology. Genes for which RNAi knockdown affected lipid droplet parameters, as indicated by the green "hit" traffic light icon on the Gene page. See experimental details on this page.
Transcriptionally regulated by ac-Lipo. Genes whose expression levels in human THP-1 macrophages were altered upon incubation with acetylated apolipoprotein B-containing lipoproteins, as determined by Mejhert et al. 2020.
LD protein in THP-1 macrophages. Proteins localized to lipid droplets in human THP-1 macrophages, as determined by Mejhert et al. 2020.
LD protein in SUM159 cells. Proteins localized to lipid droplets in human SUM159 mammary carcinoma cells, as determined by Mejhert et al. 2020.
LD protein in mouse liver. Proteins localized to lipid droplets in mouse liver, as determined by Krahmer et al. 2018.
LD protein in U2OS cells. Proteins localized to lipid droplets in the U2OS human osteosarcoma cell line, as determined by Bersuker et al. 2018.
LD protein in Huh7 cells. Proteins localized to lipid droplets in the Huh7 human hepatocellular carcinoma cell line, as determined by Bersuker et al. 2018.
2. Parameters describing the MAGMA score for a gene
MAGMA (Multi-marker Analysis of GenoMic Annotation) is a method to produce gene-level p-values for significance of the association of genes with phenotypes. MAGMA was run using the largest available genetic association dataset for each phenotype from the Knowledge Portal Network database.
MAGMA software | MAGMA publication
You may select one or two phenotypes to retrieve the MAGMA gene-level scores for each gene and phenotype. You may also specify an upper limit, a lower limit, or a range of p-values to retrieve. If you have selected two phenotypes and set a limit or range for p-values, the search will retrieve genes for which the MAGMA p-values for both phenotypes meet the specified criteria.
Viewing and editing search criteria
After you have entered parameters into the "Build filtering criteria" panel, click the "Build search criteria" button at the bottom of the panel. The top of the resulting page shows the criteria you have entered. Lipid droplet criteria are shown in blue, and MAGMA criteria are shown in yellow. Click the "x" on any criterion to remove it, or click the "Edit search criteria" button to go back to the "Build filtering criteria" panel.
Search results
When you are satisfied with your search criteria, click the "Submit search" button. The search results page presents the matching genes in tabular format. Click on any column header to sort by the values in that column.
The search results table includes the genes that answer all search criteria. In the example shown above, 557 genes were found with the lipid droplet filtering criteria, 6851 were found with MAGMA criteria, and the intersection of the two sets includes 205 genes.
If high-content imaging data exists for a gene in the search results, then additional columns will show parameters describing the number, shape, size, intensity, and dispersion of lipid droplets in human cells in which the expression of that gene had been silenced. If those parameters are not available for a gene, then "N/A" is shown.
Saving and reproducing a search
To save or share a search, copy the text shown in the "Copy to reproduce search" box.
To reproduce a search, enter this text into the "Feed search criteria manually" box on the "Build filtering criteria" panel:
