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 Jun 17;20:3359–3371. doi: 10.1016/j.csbj.2022.06.016

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

Crown Copyright © 2022 Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

PMC Copyright notice

Fig. 4 — The Sort Criteria for mining for Methylation clusters (a). Options are available to filter probe results to prioritise particular disease “Progression Stages”, the “Direction of Progression” as the “Minimum change threshold (%)” required. To facilitate assay development, methylation target regions can be specified to a particular “Cluster Length” between 100 and 250 bp. Methylation probes included can be restricted to Promoter, Gene Body, CpG Island regions or none of these. Upper and lower thresholds for considering a probe as Non-methylated/Methylated can be specified. The scoring calculation can include all probes or only those that are Methylated/Non-methylated. Probes from certain patients can be included or excluded from the scoring calculation. The Methylation clusters interface displaying results for methylation probes “From cg16265906 to cg23180938” (b). The ranked Methylation clusters and their genomic locations are presented on the left as a scrollable list. The “Apply Filter” feature can be used to search the ranked list. The “Summary of methylation progression” displays as a line, a probes methylation status across each of the patients. The methylation status of a probe during disease progression is indicated with shading that is explained in the “Methylation Colour Guide” legend. Overall mean values for the methylation cluster for disease stages for each patient are provided in the table. All probes associated with a Methylation cluster are displayed in the lower right panel and the intensity of the green shading is reflective of a probes’ score and how positively its trends in methylation related to disease progression. The panel is interactive, and a probe can be selected to examine its results in detail. After probe selection, results in the “Methylation Clusters” interface are updated with probe specific results (c). The “UCSC” button can be selected to visualise the genomic region for the CpG probe of interest utilising the online UCSC Genome browser. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)