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

. 2022 Aug 18;54(9):1355–1363. doi: 10.1038/s41588-022-01154-4

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

© The Author(s) 2022

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Extended Data Fig. 3 — The analyses were performed with the ROSMAP data (n = 832). Panel a shows the numbers of overlapping sGenes between THISTLE and sQTLseekeR. Panel b shows the numbers of overlapping sGenes considering only the SNP-gene pairs tested in common between THISTLE and sQTLseekeR. Panel c shows the number of sGenes discovered at different p-value thresholds for THISTLE and sQTLseekeR. Panel d shows the ratio of the number of sGenes identified by THISTLE to that by sQTLseekeR at different p-value thresholds. Panels e and f show the replication rates of the lead cis-sQTL SNPs at P_sQTL < 0.05 and P_sQTL < 0.05/m (where m is the number of SNPs taken forward for replication for each method), respectively. Each row represents an analysis from which the lead cis-sQTL SNPs (one SNP per gene) were identified ( $P < 5 \times 1 0^{- 8}$ ), and each column represents an analysis in which the SNPs were replicated. The THISTLE, sQTLseekeR, and LeafCutter & QTLtool p-values were computed using a one-sided sum of chi-squared test, pseudo-F test, and chi-squared test, respectively.

Source data