Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)

Abstract

PANTHER Classification System (www.pantherdb.org) is a comprehensive system that combines genomes, gene function classifications, pathways and statistical analysis tools to enable biologists to analyze large-scale genome-wide experimental data. The current system (PANTHER v.14.0) covers 131 complete genomes organized into gene families and subfamilies; evolutionary relationships between genes are represented in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models, or HMMs). The families and subfamilies are annotated with Gene Ontology terms and sequences are assigned to PANTHER pathways. A suite of tools has been built to allow users to browse and query gene functions, and analyze large-scale experimental data with a number of statistical tests. PANTHER is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. Since the protocol to use this tool (v8.0) was originally published in 2013, there have been significant improvements and updates in the areas of data quality, data coverage, statistical algorithms and user experience. This Protocol Update will provide a detailed description of how to analyze genome-wide experimental data in the PANTHER Classification System.

Association of Rare Genetic Variants in Opioid Receptors with Tourette Syndrome

“…Rare variants correspond to variant with MAF<0.01; ultrarare variants have an MAF<0.001. We used the statistical overrepresentation tests from PANTHER 14.1 35 with the “GO biological process complete” option to look for molecular pathways and functions enriched in gene lists with rare variants identified by exome sequencing in TS patients (supplementary Tables 6 and 7).…”

Nuclear encoded photosynthesis genes are specifically controlled by the NuA4 complex

“…Two of these proteins, AOG2 and BRD6, were copurified with A. thaliana NuA4 subunits previously, albeit in much larger pools of additional interactors (Table 1) 24,30,36 . Interestingly, the uncharacterized bromodomain protein BRD6 37 , previously copurified with SWC4 24 and HAM1 30 (Table 1), is orthologous to BRD8, a subunit of the human equivalent of NuA4, the TIP60/p400 complex, according to PANTHER Classification System 38,39 , indicating a possible role as an accessory subunit of the plant NuA4. AOG2, on the other hand, may be of interest in the context of the role of NuA4 in gametophyte development 36 .…”

WormCat: an online tool for annotation and visualization of Caenorhabditis elegans genome-scale data

“…WormCat.com maps annotations to input genes, then determines category enrichment 374 for Cat1, Cat2 and Cat3 (Fig 1B). Determination of category enrichment in a gene set 375 of interest compared to the entire genome can rely on several commonly used statistics 376 such as the Fisher's exact test and the Mann-Whitney test (Mi et al 2019). We used 377…”