This project reproduces the study carried out by Hittalmani S. et al. in 2016 about the S. oryzae fungus, which causes sheath rot of rice. We used OmicsBox for all necessary steps till functional analysis in order to predict pathogenic functions. (Original research paper: https://doi.org/10.1186/s12864-016-2599-0)
It is possible to run Blast only on the differential expressed genes and not on all the data with OmicsBox. One has to select only those sequences that have differential expressed genes in the OmicsBox project.First, make sure that the name of the sequences in the project match the ones from the differential expression results.
In this analysis, we will reproduce a study carried out by Michaela M. Martis et al. in 2017 with OmicsBox. (http://doi.org/10.1371/journal.pone.0185182) Introduction Ascaridia galli is an intestinal parasite that infects a wide range of domestic birds. It is especially important in European farms, where it parasites laying hens and causes economic problems. The only available treatments are the Benzimidazole derivatives,
How to combine pairwise differential expression results with a functional annotation project in OmicsBox.
Once differential expression results are retrieved, it could be interesting to assign functional annotations to the differentially expressed genes and visualize the results in a single project. This is possible in OmicsBox.
This article explains how to start functional enrichment analysis of pairwise differential genes in Blast2GO.
This article explains how to create ID lists of either Blast results or differential expressed genes in Blast2GO.
This article explains what a Gene Set Enrichment Analysis (GSEA) is, how it works and how to use it with OmicsBox. What is an enrichment analysis? Enrichment analyses are a family of bioinformatics methods that aim to facilitate the biological interpretation of many bioinformatics results. Among these, the methods based on gene sets analysis are particularly helpful and widespread. The
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