PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification

By Paul D. Thomas, Anish Kejariwal, Michael J. Campbell, Huaiyu Mi, Karen Diemer, Nan Guo, Istvan Ladunga, Betty Lazareva-Ulitsky, Anushya Muruganujan, Steven Rabkin and 2 more. Nucleic Acids Res., 2003

682 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d54f108735c9edba1f7aba118a27a7ff99d679d7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

The PANTHER database of protein families, subfamilies, functions and pathways (2004, methodology): “0 (1,2) used seed-based clustering to define protein families.”
The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra*S (2007, background): “…on two different FASTA format protein databases, the UniProtKB/Swiss-Prot database, which has about 200,000 proteins, and the CDS Combined file (35, 36), which is essentially a version of National Center for Biotechnology Information (NCBI) NR.fas that has been made truly non-redundant for public…”
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools (2018, background): “PANTHER is a comprehensive resource for classification of genes according to their evolutionary history, and their functions (1,2).”
Improving the prediction of disease-related variants using protein three-dimensional structure (2011, methodology): “These algorithms are able to predict the effect of the mutation on protein stability [13,14,19,23-26], protein functional activity [9,21], and insurgence of human pathologies [7,8,10-12,1518,20-22].”
A Map of Recent Positive Selection in the Human Genome (2006, methodology): “The PANTHER Gene Ontology database provides a classification of genes into 222 nested categories according to biological process [41].”
Finding Homologs in Amino Acid Sequences Using Network BLAST Searches (2003, background): “Examples for such a region include coiled coils, leucine-rich repeats, ATP-binding domains, epidermal growth factor domains, and myosin and other domains, which serve as widespread building blocks of diverse proteins (Finn et al., 2016; Thomas et al., 2003).”
PANTHER Pathway: an ontology-based pathway database coupled with data analysis tools (2009, methodology): “The core of the system is a large collection of phylogenetically defined protein families and subfamilies generated by computational algorithms, and curated by expert biologists using an extensive software system for associating ontology terms (Thomas et al. 2003).”
PANTHER: a library of protein families and subfamilies indexed by function. (2003, background): “…and searching by either function or family/subfamily terms, and access to the multiple alignment and sequence-based tree representation of each family, as well as lists of all proteins in a given organism that belong to a given family or subfamily (Thomas et al. 2003; http://panther.celera.com).”