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Table 1 Summary of the types of data integrated in phylogenomics databases

From: Phylogenomics databases for facilitating functional genomics in rice

Data type Providing information or data Reference
Sequence locus IDs from MSU-RGAP and The Rice Annotation Project Database (RAP-DB; http://rapdb.dna.affrc.go.jp/), family and sub-family names, domain positions, NCBI blast result (IRGSP 2005; Yuan et al. 2005)
Sequence Quality TE-relatedness, existence of EST/cDNA, and Program to Assemble Spliced Alignments (PASA) status  
Orthologs in Plants orthologs from 12 plant species, (i.e., Brachypodium distachyon, Panicum virgatum, Sorghum bicolor, Zea mays, Arabidopsis thaliana, Cucumis sativus, Glycine max, Medicago truncatula, Mimulus guttatus, Populus trichocarpa, Ricinus communis, and Vitis vinifera) (Berglund et al. 2008)
Topology Transmembrane Domain (TM), N-terminal Myristoylation Site (Myrist), N-terminal Signal Peptide (SignalP), Chloroplast Transit Peptide (ChloroP), and predicted Subcellular Localization  
Mutants mutant lines and corresponding flanking sequence tags from eight institutes (Chandran and Jung 2014)
Interactome Data experimentally validated network of protein–protein interactions based on Yeast Two-Hybrid (Y2H) and Tandem Affinity Purification (TAP) methods (Ding et al. 2009)
Digital Northern Data normalized frequency of ESTs in selected tissues/organs (Dardick et al. 2007; Jung et al. 2010)
MPSS mRNA Data meta-expression data from 70 libraries (Nakano et al. 2006)
MPSS Small RNA Data meta-expression data from six libraries (Nakano et al. 2006)
Microarray Data meta-expression data from the six microarray platforms including Affymetrix, Agilent22K, Agilent44K, BGI/YALE60K, NSF20K, and NSF45K (http://ricephylogenomics.ucdavis.edu/description.shtml) (Cao et al. 2012)