Our manual curation includes a review of the experiment description and the related publication to understand experimental design; combines data from replicates; and creates pair-wise comparisons or contrasts as described in the publication to identify differential gene expression, data normalization and log-transformation. Available analyses consist of a suite of integrated tools to explore, visualize and compare a large number of published transcriptomics datasets. PATRIC also allows researchers to upload and analyze their own gene expression data in their private workspace and compare it to existing data. Learn more in our Transcriptomics FAQs.
PATRIC has three primary types of experiment data, Taxonomy or Genome level, Gene or CoDing Sequence level, and Your Own Uploaded Experiment data.Â Learn about these types of experiment data, where you can find them, and some of the potential analyses you can do.
Follow us step-by-step as we take you through finding a hypothetical protein to explore, examining the hypothetical gene of interest, and looking for expression patterns across a group of correlated genes.
See how to use PATRIC tables and the Table Toolbar including sorting, downloading, analysis tools, creating persistent column customization, and saving items to your workspace.
We use transcriptomics analysis at different taxonomic levels to find significant expression patterns that could help to infer gene function.Â Specifically, here we find genes that are highly expressed in an anaerobic environment at the organism level and then look for similar expression patterns at the gene level.Â Finding evidence that a gene is highly expressed in multiple experiments utilizing a low-oxygen environment could indicate that it impacts survival of the bacterium in the intracellular environment.
With Pathogen Portal’s RNA-Rocket you can align your Illumina fastQ reads against supported genomes, view supported genomes, and estimate gene expression values.Â This tutorial provides an overview of creating an account, exploring the site, getting data, checking quality, starting analysis, and further analysis.
Find out more about PATRIC data, analysis tools, and functionality in our Frequently Asked Questions.