PANTHER Tutorial 2011.Pptx
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PANTHER Version 11: Expanded Annotation Data from Gene Ontology and Reactome Pathways, and Data Analysis Tool Enhancements
Published online 28 November 2016 Nucleic Acids Research, 2017, Vol. 45, Database issue D183–D189 doi: 10.1093/nar/gkw1138 PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements Huaiyu Mi*, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang and Paul D. Thomas* Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA Received October 05, 2016; Revised October 27, 2016; Editorial Decision October 28, 2016; Accepted November 16, 2016 ABSTRACT INTRODUCTION The PANTHER database (Protein ANalysis THrough Protein ANalysis THrough Evolutionary Relationships Evolutionary Relationships, http://pantherdb.org) (PANTHER) is a multifaceted data resource for classifica- contains comprehensive information on the evolu- tion of protein sequences by evolutionary history, and by tion and function of protein-coding genes from 104 function. Protein-coding genes from 104 organisms are clas- completely sequenced genomes. PANTHER software sified by evolutionary relationships, and by structured rep- resentations of protein function including the Gene Ontol- tools allow users to classify new protein sequences, ogy (GO) and biological pathways. The foundation of PAN- and to analyze gene lists obtained from large-scale THER is a comprehensive ‘library’ of phylogenetic trees genomics experiments. In the past year, major im- of protein-coding gene families. These trees attempt to re- provements include a large expansion of classifica- construct the evolutionary events (speciation, gene duplica- tion information available in PANTHER, as well as tion and horizontal gene transfer) that led to the modern- significant enhancements to the analysis tools. -
Exploring the Roles of Horizontal Gene Transfer in Metazoans by Dongliang Chen June, 2016 Director: Dr. Jinling Huang DEPARTMEN
Exploring the Roles of Horizontal Gene Transfer in Metazoans By Dongliang Chen June, 2016 Director: Dr. Jinling Huang DEPARTMENT OF BIOLOGY Horizontal gene transfer (HGT; also known as lateral gene transfer, LGT) refers to the movement of genetic information between distinct species by overcoming normal mating barriers. Historically HGT is only considered to be important in prokaryotes. Some researchers believe that eukaryotes have sexual recombination and HGT is insignificant. However, HGT has also been found to play roles in many aspects of eukaryotic evolution, like parasitism and the colonization of land by plants, although at lower frequencies than in prokaryotes. In this dissertation, I first estimated the scope of HGT in 16 selected metazoan species by genome screening using AlienG. These species are sampled to represent major lineages of metazoans. Among all the 16 species, Nematostella vectensis (4.08%) has the highest percentage of HGT genes, while parasitic Schistosoma japonicum (0.47%) ranks the lowest. In order to find out which factors are correlated with HGT rates in different species, living habitat, diet, lineage group and reproductive type were analyzed in a statistical framework. In Chapter 3 and Chapter 4, Ciona intestinalis and Trichoplax adhaerens were chosen as models to investigate horizontally acquired genes. Tunicate cellulose synthase was discovered to originate from green algae, instead from bacteria as found in previous studies. 43 genes of 21 families in T. adhaerens were found to be horizontally acquired. -