Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2021 Jan 12;22:22. doi: 10.1186/s12859-020-03929-0

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

PMC Copyright notice

Fig. 2 — Overview of the dpGSEA pipeline and enrichment approach. Beginning from the left side of the diagram, the two primary inputs of dpGSEA are shown as tables. The top left table lists DEGs from, for example, a disease versus control study. The bottom left table contains the proto-matrix, which is analogous to MSigDB defined gene sets but contains a list of drug-gene actions rather than a gene set. dpGSEA merges the information in these tables by gene and ranks them by the absolute value of their significance. dpGSEA then estimates a running sum statistic based on drug-gene interaction and regulation. Highlighted in yellow are negatively correlated drug-gene interactions (opposing arrows). Enrichment distributions are formed [dotted red line, enrichment score (ES)] determining the maximum deviation of the running sum statistic plot, while the position of the maximum deviation (dotted orange line) represents the target compatibility score (TCS). dpGSEA then permutes the gene locations and generates new enrichment distributions along with null-enriched ES and TCS. The permutations are used to both normalize and generate statistical significance for each score. The output is a list of drugs ranked by their ES or TCS statistical significance (bottom center table). It should be noted that leading-edge genes are also included in the output (not shown)