Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures

Bioinformatics
Zichen WangAvi Ma'ayan

Abstract

Mechanistic molecular studies in biomedical research often discover important genes that are aberrantly over- or under-expressed in disease. However, manipulating these genes in an attempt to improve the disease state is challenging. Herein, we reveal Drug Gene Budger (DGB), a web-based and mobile application developed to assist investigators in order to prioritize small molecules that are predicted to maximally influence the expression of their target gene of interest. With DGB, users can enter a gene symbol along with the wish to up-regulate or down-regulate its expression. The output of the application is a ranked list of small molecules that have been experimentally determined to produce the desired expression effect. The table includes log-transformed fold change, P-value and q-value for each small molecule, reporting the significance of differential expression as determined by the limma method. Relevant links are provided to further explore knowledge about the target gene, the small molecule and the source of evidence from which the relationship between the small molecule and the target gene was derived. The experimental data contained within DGB is compiled from signatures extracted from the LINCS L1000 dataset, the orig...Continue Reading

References

Apr 25, 2006·Biostatistics·W Evan JohnsonAriel Rabinovic
Nov 10, 2013·Nucleic Acids Research·Vivian LawDavid S Wishart
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
Sep 27, 2016·Nature Communications·Zichen WangAvi Ma'ayan
May 26, 2018·Nucleic Acids Research·Daniel J B ClarkeAvi Ma'ayan

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