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 use case we will use the metagenomics tools included in OmicsBox to analyze the microbial communities of two different soda lakes from Brazil. The original study was carried out by Ana P. D. Andreote, et al., 2018 (doi: 10.3389/fmicb.2018.00244). Introduction Soda lakes are special ecosystems found across Africa, Europe, Asia, etc. These lakes show high levels of sodium
OmicsBox Supported Project Researchers: Background and Project Overview: A.baumannii, a nosocomial pathogen, ranks first in the WHO’s list of antibiotic-resistant priority pathogen. The problem of increasing frequency of multi-drug resistance in A. baumannii has been further compounded by tolerance to high concentration of antibiotics due to persister cells. Persister cells are phenotypic variants of normal cells that are formed in
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.
BioBam Bioinformatics S.L. Supported Project. Researchers: Nahid Hosseinzadeh Gharajeh Mohammad Amin Hejazi Mostafa Valizadeh Ebrahim Dorani Background and Project Overview: Dunaliella is a unicellular, halotolerant, biflagellate microalga which is already exploited as a platform in food, feed, aquaculture, biomedical, pharmaceutical, nutraceutical and cosmeceutical industries, specifically due to its high production of β-carotene and fine chemicals. There is a wide range
Release Date: 13/01/2018) Just in time for the PAG Plant & Animal Genome Conference, we launched Blast2GO 5! This major release brings many new features. Most importantly, Blast2GO is now connected to the powerful BioBam Cloud, an AWS architecture which gives a big boost to many analysis steps. Details below. To upgrade from version 4 to 5 you have to
The Time Course Expression Analysis tool allows performing a differential expression analysis of expression data arising from a time course RNA-seq experiment. This application is based on the maSigPro Bioconductor package, which implements a two-step regression strategy to detect genes with significant temporal expression changes and significant differences between experimental groups. This video shows the analysis of count data coming
The Pairwise Differential Expression Analysis tool is designed to perform differential expression analysis of count data arising from an RNA-seq experiment. The application, which is based on the software package “edgeR”, allows the identification of differentially expressed genes between two experimental conditions by applying quantitative statistical methods. This video shows the performance of a pairwise differential expression analysis in which
