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

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)