Contents
1. Introduction
Ciliate protozoa, a major component of eukaryotic microorganisms, play crucial ecological roles, serving as both predators and prey in aquatic ecosystems, significantly contributing to material recycle and energy flow. Despite the significant ecological importance of ciliates, the study of their functional genomes has been challenging due to that ciliates always have complex genetics and most of them are unculturable. Thanks to the advances in gene and molecular manipulation techniques, a few culturable ciliates such as Tetrahymena thermophila, Paramecium tetraurelia and Oxytricha trifallax have developed relatively advanced experimental techniques. With the development of sequencing technology, an increasing amount of omics data from ciliates has become available. When integrated with bioinformatics analyses, these data have provided significant insights into biological evolution. Moreover, the ongoing exploration of ciliates has further contributed to the surge in omics data, creating a need for specialized databases to effectively organize and analyze this information.
Herein, we developed CiliateBase, a pioneering platform that consolidates extensive data from curated RNA-seq, ChIP-seq, MNase-seq, and RIP-Seq datasets linked to 96 target genes manipulated by diverse KO/KD methods across Tetrahymena thermophila, Paramecium tetraurelia and Oxytricha trifallax. It serves as a platform for storing and analyzing the regulatory networks of functional genes in ciliates. In addition, CiliateBase has integrated published genome data from various species and functional annotations were achieved by using EggNOG-mapper, which uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Therefore, CiliateBase will serve as a powerful tool in the study of potential molecular functions of these fascinating organisms.
2. Web interface of CiliateBase
2.1 How to search CiliateBase?
Users can search through two ways including 'quick search' and 'browse' as shown below.
2.2 Search Result
Search result including 'primary' and 'detail' sections as shown below.
2.3 JBrowse
JBrowse is a powerful and user-friendly functional module in our database website. It is mainly used for visualizing and analyzing genomic data of ciliates. With JBrowse, users can easily browse the genomic sequences of ciliates, zoom in and out to view details at different scales. It allows users to identify specific genes, regulatory elements and other important genomic features. Meanwhile, JBrowse can display various genomic annotations, such as exon-intron structures, protein - coding regions, helping users better understand the genomic information of ciliates. In addition, this module supports the comparison of peak data among different datasets.
2.4 BLAST
CiliateBase integrates a BLAST sequence alignment feature, which aims to provide efficient sequence analysis services for researchers worldwide and to further propel ciliate-related scientific investigations. This functionality empowers users to rapidly identify homologous sequences within the ciliate genomic data repository, thus facilitating taxonomic identification, gene function prediction, and evolutionary studies.
2.5 Enrichment Server
CiliateBase incorporates an effective online tool for functional gene enrichment analysis. This tool is designed to help researchers gain a deeper understanding of the biological significance of the genes identified in ciliate functional genomics studies. The functional gene enrichment analysis, which encompasses GO (Gene Ontology) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment, is powered by the highly efficient software, clusterProfiler.
