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

. 2020 Feb 5;3:56. doi: 10.1038/s42003-019-0741-7

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

© The Author(s) 2020, corrected publication 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

Fig. 4 — a Panel showing a hypothetic feature analysis example to illustrate the content of the following figures. All panels in this figure display features (dots), plotted by their log-fold difference (odds ratio in case of panel (b)) between CLC/non-CLC genesets (y-axis) and statistical significance (x-axis). In all plots dark and light green dashed lines indicate 0.05 and 0.01 significance thresholds, respectively. b Cancer and non-cancer disease-related data from indicated sources: y-axis shows the log2 of the odds ratio obtained by comparing CLC to non-CLC by Fisher’s exact test; x-axis displays the estimated p-value from the same test. “CGC 1 kb TSS” refers to the fraction of genes that have a nearby known CGC cancer protein-coding gene. This is explored in more detail in the next Figure. “Non-cancer SNPs” refers to GWAS SNPs associated with diseases/traits other than cancer. c Sequence and gene properties: y-axis shows the log2 fold difference of CLC/non-CLC means; x-axis represents the p-value obtained. d Evolutionary conservation: “Phastc mean” indicates average base-level PhastCons score; “Elements” indicates percent coverage by PhastCons conserved elements (see Methods). Colours distinguish exons (blue) and promoters (purple). e Tumour RNA-seq: expression levels of lncRNA genes in different cancer tissues obtained from RNA-seq expression data from PCAWG. For (b–d), statistical significance was calculated using Wilcoxon test.