Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics.
Tomato Functional Genomics Database (TFGD) provides a comprehensive resource to store, query, mine, analyze, visualize and integrate large-scale tomato functional genomics data sets. The database is functionally expanded from the previously described Tomato Expression Database by including metabolite profiles as well as large-scale tomato small RNA (sRNA) data sets. Computational pipelines have been developed to process microarray, metabolite and sRNA data sets archived in the database, respectively, and TFGD provides downloads of all the analyzed results. TFGD is also designed to enable users to easily retrieve biologically important information through a set of efficient query interfaces and analysis tools, including improved array probe annotations as well as tools to identify co-expressed genes, significantly affected biological processes and biochemical pathways from gene expression data sets and miRNA targets, and to integrate transcript and metabolite profiles, and sRNA and mRNA sequences. The suite of tools and interfaces in TFGD allow intelligent data mining of recently released and continually expanding large-scale tomato functional genomics data sets. TFGD is available at http://ted.bti.cornell.edu.
Boyce Thompson Institute for Plant Research, Cornell University, USDA Robert W Holley Center for Agriculture and Health, Ithaca, NY 14853, USA. zf25@cornell.edu
Zhangjun
Z
Fei
Je-Gun
JG
Joung
Xuemei
X
Tang
Yi
Y
Zheng
Mingyun
M
Huang
Je Min
JM
Lee
Ryan
R
McQuinn
Denise M
DM
Tieman
Rob
R
Alba
Harry J
HJ
Klee
James J
JJ
Giovannoni
D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018745:Genome, Plant; D023281:Genomics; D018551:Solanum lycopersicum / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000378:metabolism
D058727:RNA, Small Untranslated