The Combined Pathway Analysis in OmicsBox maps sequences to Reactome, Plant Reactome and KEGG in a single run. Since version 4.1, it also supports WikiPathways.
What is WikiPathways
WikiPathways is an open, community-curated pathway database founded in 2008 (Agrawal et al., Nucleic Acids Research 2024).
The results of a pathway analysis depend on the database used. KEGG and Reactome are curated by central teams, and their coverage of some biological processes and organisms is limited. WikiPathways follows a different model: researchers contribute and update pathways directly, and the content is reviewed by the community. New data releases are published monthly, and all content is available under a CC0 license.
Main advantages:
- Open: freely reusable content, with no licensing restrictions.
- Up to date: continuous community curation and monthly releases.
- Complementary coverage: pathways for processes, diseases and species that are underrepresented in other resources.
WikiPathways is most useful as a complement to KEGG and Reactome. Running it in the same analysis shows whether results are consistent across databases and can reveal pathways that the other resources do not describe.
How to use WikiPathways in OmicsBox
WikiPathways is available in OmicsBox, a desktop application for NGS data analysis that requires no programming. In the Combined Pathway Analysis, WikiPathways can be selected alone or together with Reactome, Plant Reactome and KEGG. Running them together produces a single, unified project containing pathway evidence from all selected databases, so results can be compared and explored in one place instead of across separate tools.
The tool is located under Functional Analysis → Combined Pathways Analysis, or under Pathway Analysis in the side panel of a functional annotation project. To run the analysis you need:
- Sequences: nucleotide or protein sequences, typically in a FASTA file, or standard sequence identifiers that can be matched directly to the database.
- A linking method: BLAST against the UniProt proteins referenced in WikiPathways (recommended), or direct matching when sequence names are UniProt, Ensembl or HGNC identifiers.
The View species coverage option shows how well the target species is represented before the run. The analysis can also be restricted to selected pathway categories to reduce the multiple-testing burden.
Monitoring the analysis progress
The analysis runs on the OmicsBox cloud, so no local database download or search tool installation is required. Large sequence sets are processed faster than on a local computer.
With CloudSync, OmicsBox only needs to be open to configure and submit the job. OmicsBox can then be closed and the computer shut down while the analysis continues in the cloud. An email notification can be requested when the job finishes, and results can be saved to Cloud Files to open them from any device signed in with the same account.
With OmicsBox Web, the progress of an analysis can be checked at any time and from anywhere: a laptop, tablet or phone with a browser is enough, with no installation. The Jobs page shows the status, progress, run time and logs of each analysis, and running jobs can be cancelled. Once the job is done, results such as charts and pathway diagrams can be previewed directly in the browser and downloaded, so a first look at the results does not have to wait until you are back at your desk.
Results
WikiPathways results are reported together with those from the other selected databases in a combined results table. A Database column identifies WikiPathways entries, and extra columns record whether each sequence was linked by BLAST or by identifier. The table and all pathway diagrams can be exported in standard formats for use in other tools or in publications.
Within OmicsBox, results can be explored further:
- Pathway diagrams: Show Pathway Diagram (right-click) opens the WikiPathways map with zoom, minimap, and tooltips listing interactions and linked sequences.
- Expression overlay: differential expression results from edgeR, DESeq2, NOISeq or maSigPro are displayed as a heatmap on map elements. This shows at a glance which steps of a pathway are up- or down-regulated.
- Enrichment analysis: Fisher’s Exact Test or Gene Set Enrichment Analysis (GSEA), run from the side panel. It identifies the pathways most significantly affected in the experiment, based on a list of genes of interest (Fisher) or a ranked gene list (GSEA).
- Summary report and charts: configurable charts summarize the results and can be exported as images.
Availability
WikiPathways support is available in the Combined Pathway Analysis of the Functional Analysis module. Details are in the Combined Pathway Analysis user manual.
Reference: Agrawal A et al. WikiPathways 2024: next generation pathway database. Nucleic Acids Research 52(D1), D679–D689 (2024).