TetraFGD is a web-accessible functional genomics database of the model protozoan, Tetrahymena thermophila. Currently, TetraFGD provides RNA-seq DATA, MICROARRAY DATA and GENE NETWORK of T. thermophila. TetraFGD is funded by the Institute of Hydrobiolgy, Chinese Academy of Sciences and is headed by Dr. Wei Miao, the principal investigator (PI) of the Laboratory of Protozoan Functional Genomics.
During 2007-2008, a microarray platform in Tetrahymena thermophila was established (Microarray analyses of gene expression during the Tetrahymena thermophila life cycle. Miao W, Xiong J, Bowen J, Wang W, Liu Y, Braguinets O, Grigull J, Pearlman RE, Orias E, Gorovsky MA. PLoS ONE. 2009;4(2):e4429.). The genome-wide gene expression data of T. thermophila at 20 time points during growth (~1 X 105 cells/ml, ~3.5 X 105 cells/ml and ~1 X 106 cells/ml), starvation (at 0, 3, 6, 9, 12, 15 and 24 hours) and conjugation (at 0, 2, 4, 6, 8, 10, 12, 14, 16 and 18 hours after mixing) were completed by the Gorovsky lab at the University of Rochester, the Miao Lab at the Institute of Hydrobiolgy, Chinese Academy of Sciences and the Pearlman Lab at York University. The gene expression profiles and candidate co-expressed genes for each gene can be retrieved using Gene ID or Gene description searches in TetraFGD.
In 2010, Tetrahymena gene network (TGN) was constructed using the context likelihood of relatedness (CLR) algorithm based on microarray data from the Gorovsky lab, the Miao Lab, the Pearlman Lab and the Liu lab (University of Michigan Medical School) (Xiong J, Yuan D, Fillingham JS, Garg J, Lu X, Chang Y, Liu Y, Fu C, Pearlman RE, Miao W: Gene Network Landscape of the Ciliate Tetrahymena thermophila. Plos One 2011, 6(5):e20124.).
In 2011, RNA-seq data were obtained form six RNA samples of T. thermophila (growth: ~3.5 X 105 cells/ml; starvation: 3 and 15 hours; conjugation: 2 and 8 hours after mixing) using Illumina deep RNA sequencing by the Miao Lab. About 14 gigabases (Gb) of data covered more than 96% of the predicted genes. These data were used to correct the structural annotation of thousands of gene models and to identify more than 1,000 new transcribed regions. The transcripts can be access using Gbrowse or Blast in TetraFGD.
TetraFGD will be extended to develop/collect other functional genomics data (e.g. proteome) of Tetrahymena and is intended to be a resource for all members of the scientific research community interested in Tetrahymena. As we develop TetraFGD, we would greatly appreciate input from the community so that we can better tailor it to meet your needs. Please feel free to send comments, suggestions, or questions to TetraFGD@ihb.ac.cn.
Wei MIAO, PhD
Professor, Principal Investigator
firstname.lastname@example.org ; email@example.com
Principal Database Administrator