Bioinformatics #1 : 3 user-friendly bioinformatics applications for functional enrichment analysis

This week I will not write about review a research article but don’t worry, I still write that section in the future. It’s just this week is quite hectic but I have something to help improve your research quality if you’re dealing with bioinformatics related matter.

Nowadays, bioinformatics is important in any biology-related research field. Bioinformatics analysis can be conducted in many ways from sequencing analysis, transcriptomics, proteomics, lipidomics, and metabolomics analysis as well. In this article, I will focus more on transcriptomics analysis because scientist without programming knowledge usually fears this analysis but this analysis is popular recently that will help your research get accepted in high impact factor.

In transcriptomics analysis, there are three main parts of analysis. First, quality control that will detect some noise in your result and it will be removed. There are many software and programming package available for quality control. Second, differential expression (DE) genes analysis which will identify significant genes whether it is upregulated (expression higher than control) or downregulated (expression lower than control). The last part, after you identify the significant genes, you will check genes function in biological role. This part is called functional enrichment analysis and many users are afraid it will take complicated programming skill to conduct this analysis.

Actually, there are a lot of web-based applications that allow users to analyze their data easily even without programming knowledge. Here I make the list for you if you want to do functional enrichment analysis but you don’t have programming background:

1. Metascape
2. DAVID
3. PANTHER

1. Metascape

Source: https://metascape.org/gp/index.html#/main/step1

Metascape is a popular and highly citated web-based application for functional enrichment analysis. The main point in this web-application is they want to make “one-click application” which makes the user just click one time and complete analysis will be shown (Zhou, et al., 2019). This website provides tutorial easily to the beginner user and all you need is just put gene list to do functional enrichment analysis.

2. DAVID

Source: https://david.ncifcrf.gov/

DAVID is a classic web application and one of the most oldest functional enrichment program on the internet. This website has been existed since 2003 (Now you know why their user interface is kinda vintage). Basically, this website was almost same like Metascape but the difference is they provided multiple methods to conduct adjusted p-value score. Furthermore, DAVID provides function clustering analysis that you can’t see in Metascape. They mentioned that you can put a large gene list and the program can analyze your data with pretty detail result (Huang, et al., 2007).

3. PANTHER

Source: http://pantherdb.org/

PANTHER is another functional enrichment web-based application that has been proved it could analyze gene expression wet lab experiment (Mi & Thomas, 2009). The application provides the complete view and the lite view. Lite view is the brief result from your input gene analysis. Sometimes, you need this lite view because your result maybe is redundant and you don’t know which function is important for your analysis. What makes PANTHER different than the others is they don’t only provide functional enrichment analysis but also sequence analysis which makes them a flexible bioinformatics web tool.

Overall, the 3 web based application allow the user without programming knowledge analyze their data in complete and detail result. All they need to do is just put their DE gene list and the “ready to be published” result will show up. The user does not need to worry about programming skill but they still need to worry how to interpret the result (which I will explain in the next bioinformatics article section).

References

1. Zhou, Y., Zhou, B., Pache, L. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 10, 1523 (2019). https://doi.org/10.1038/s41467-019-09234-6
2. Huang, D.W., Sherman, B.T., Tan, Q. et al. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 8, R183 (2007). https://doi.org/10.1186/gb-2007-8-9-r183
3. Mi, H., & Thomas, P. (2009). PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods in molecular biology (Clifton, N.J.), 563, 123–140. https://doi.org/10.1007/978-1-60761-175-2_7