PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

By Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D. Thomas. 2016

1,995 citations recorded by the source corpus.

The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org) contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools. Protein subfamily functional classifications have more than doubled due to progress of the Gene Ontology Phylogenetic Annotation Project. For human genes (as well as a few other organisms), PANTHER now also supports enrichment analysis using pathway classifications from the Reactome resource. The gene list enrichment tools include a new ‘hierarchical view’ of results, enabling users to leverage the structure of the classifications/ontologies; the tools also allow users to upload genetic variant data directly, rather than requiring prior conversion to a gene list. The updated coding single-nucleotide polymorphisms (SNP) scoring tool uses an improved algorithm. The hidden Markov model (HMM) search tools now use HMMER3, dramatically reducing search times and improving accuracy of E-value statistics. Finally, the PANTHER Tree-Attribute Viewer has been implemented in JavaScript, with new views for exploring protein sequence evolution.

Subfields: Molecular Biology

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Citations in the corpus

Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, methodology): “H. Mi et al., PANTHER version 11: Expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.”
YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, methodology): “…2016 https://pachterlab.github.io/kallisto/ Deseq2 Love et al., 2014 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html PANTHER GO Mi et al., 2013, 2017 http://pantherdb.org Origami This study https://github.com/younglab/origami Cell Ranger 10X Genomics…”
The Gene Ontology of eukaryotic cilia and flagella (2017, methodology): “For example, the PANTHER online resource [9] hosts a tool to perform GO enrichment analysis on user-defined gene sets, to help identify the biological processes or cellular components enriched in the set.”
Pi-Pi contacts are an overlooked protein feature relevant to phase separation (2018, methodology): “Phase separation critical concentration values for the N-terminus (1-236) of human Ddx4 and three mutants, 9FtoA and 14FtoA, as reported in (14), and RtoK, where all arginine residues have been mutated to lysine, as well as for the C-terminus (445-632) of human FMR1 and one mutant with all arginine ”
Intrinsically disordered proteins and structured proteins with intrinsically disordered regions have different functional roles in the cell (2019, methodology): “157 Clustering of the variants of disorder through functional profiles 158 The functional profiles of ORDPs, IDPRs and IDPs were defined considering several annotations, 159 such as: biological processes, cellular components and molecular functions from the Gene Ontology 160 database [52] and protei”
Ensembl 2020 (2019, background): “Variants co-located with a transcript can be displayed and coloured according to their SIFT (41) or PolyPhen-2 (42) predicted pathogenicity alongside exon boundaries and protein domains from Gene3D (43), Smart (44), Pfam (45) and Panther (46).”
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes (2019, methodology): “pyHam can also be used to infer enhanced phylogenies for other datasets available in OrthoXML format such as ENSEMBL [13] or with data generated from phylogenetic trees such as those found in PANTHER [64] through the use of the function etree2orthoxml () in the tree analysis package ETE3 [65].”
20 years of the SMART protein domain annotation resource (2017, background): “Despite the focus shift in bioinformatics towards comparative genomics, transcriptomics and network biology, protein domain analysis remains an essential and important research tool, made easy by various frequently used online domain resources and databases, like Pfam (13), PANTHER (14) or PROSITE (”
Expansion of the Gene Ontology knowledgebase and resources (2016, methodology): “This enables users to take advantage of the PANTHER visualization tools, such as the new hierarchical view that organizes enrichment analysis results using the relations in the GO (18).”
OMA standalone: orthology inference among public and custom genomes and transcriptomes (2018, neutral): “2006), PANTHER (Mi et al. 2017), PhylomeDB (Huerta-Cepas et al.”
PANTHER: Making genome‐scale phylogenetics accessible to all (2021, methodology): “20 Users can specify flanking regions on either side of the gene, so if the variant is outside of the gene region but within the flanking region of the gene, it can be assigned to the gene as well.”
The Reactome Pathway Knowledgebase (2017, background): “A variety of online resources capture aspects of this information at the level of individual reactions such as Rhea (1) or at the level of reaction sequences spanning various domains of biology such as KEGG (2), MetaCyc (3) or PANTHER (4).”
The Aging Astrocyte Transcriptome from Multiple Regions of the Mouse Brain (2018, methodology): “Gene ontology annotation was performed using PANTHER version 12 (Mi et al., 2017) using input data as described for Table S5 (genes with >50% change between adult and aged, FPKM of >0.5, expressed at least 0.75- fold of input).”