TrichOME V3: A Comparative Omics Database for Plant Trichome
The TrichOME database has been updated in October 2012. To visit previous version, please click here.
- Added 30 Sanger EST libraries and 11 Roche 454 EST libraries.
- Assembled EST sequences using 454 Newbler instead of TIGR assembler.
TrichOME is an integrated genomic database of genes and metabolic pathway in plant trichomes. Comprehensive data hosted in the TrichOME were mainly generated through a NSF-funded project (Award #0605033) and also collected from various public resources, e.g. from NCBI's sequence repositories and ArrayExpress database. TrichOME hosts integrated information including:
EST sequences: TrichOME hosts 4,230,576 Sanger/454 ESTs sequenced from 16 species. These ESTs were sequenced from trichome and non-trichome control tissues; the latter were included for improving assembly quality and comparative genomics analysis. These ESTs were assembled into 53,835 trichome-related TC and further annotated on the basis of UniProtKB / TrEMBL, Gene Ontology database, KEGG pathway database, TCDB transporter database and transcription factor database. All of ESTs, including Sanger ESTs and 454 ESTs, are available for download, while only Sangle ESTs are able to be searched by keywords and treeview style browser. We also implemented an in-silicon gene expression analysis tool for searching trichome-specific genes.
Microarray hybridizations: TrichOME hosts hybridizations from Arabidospsis thaliana, Medicago truncatula, and Medicago sativa (Alfalfa). These hybridizations were performed on glandular trichome, non-glandular trichome and control tissues using Affymetrix genechip. Both raw hybridization signals and pre-normalized expression signals are available for batch download and individual search. A set of tools were also developed to facilitate the analysis and mining of trichome-related genes.
Mass spectrometry-based metabolite profiles: The TrichOME hosts gas chromatography-mass spectrometry (GC-MS) data sampled from two cultivars of Medicago sativa and Humulus lupulus. More data will be added into the database as the experiments progress.
Literature mining and curation: We've curated over 1,000 literatures to mine trichome-related genes and proteins.
We've implemented AJAX-based web interface to facilitate interactive searching and mining of ESTs / Unigenes, Microarray gene expression, metabolite and literature data. This system would be very useful for discovering the relationship between genes, pathways and metabolites in trichomes. The TrichOME has been publicly available since December, 2007, which is being actively used by our collaborators as well as a broader trichome research community. This database is freely open to all users and there is no login requirement.
|Funding by the National Science Foundation
|Additional funding by The Samuel Roberts Noble Foundation