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

. 2018 Nov 25;34(1):5–18. doi: 10.1177/0748730418813785

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

© 2018 The Author(s)

This article is distributed under the terms of the Creative Commons Attribution 4.0 License (http://www.creativecommons.org/licenses/by/4.0/) which permits any use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage).

PMC Copyright notice

Figure 1. — Using LimoRhyde to analyze circadian transcriptome data from livers of wild-type and Arntl^{^-/-} mice under night-restricted feeding (GSE73552). (A) Scatterplot of -log₁₀(q_DR) vs. Δamplitude. q_DR corresponds to a rhythmic gene’s q-value of differential rhythmicity. Δamplitude corresponds to the change in rhythm amplitude between genotypes, where a negative value indicates lower amplitude in Arntl^-/-. In A-C, each point represents a gene. In A and B, the 16 rhythmic genes with the highest -log₁₀(q_DR) are labeled. (B) Scatterplot of -log₁₀(q_DR) vs. Δacrophase. The latter corresponds to the change in zeitgeber time of peak expression, where a positive value indicates a phase advance in Arntl^-/-. Only genes with q-value for rhythmicity in both genotypes ⩽ 0.2 are shown. (C) Scatterplot of -log₁₀(q_DE) vs. log₂ (fold-change). q_DE corresponds to the q-value of differential expression. A positive log₂ (fold-change) indicates higher average expression in Arntl^-/-. The 10 genes with the highest -log₁₀(q_DE) are labeled. (D) Venn diagram of genes meeting criteria for rhythmicity (q-value of rhythmicity q_rhy ⩽ 0.01), differential rhythmicity (q_DR ⩽ 0.1), and differential expression (q_DE ⩽ 0.1). (E) Plots of 3 example genes. Each point represents a sample. Based on the criteria, Per2 is classified as rhythmic only, Per3 as differentially rhythmic, and Hectd2 as differentially expressed only.