miRNA target genes that were supported by two databases (TarBase and miRecords) with experimental evidence were retrieved for pathway analysis.
Among the 15 predicted associations by our method, all have been successfully identified, five of which are commonly confirmed by two databases.
We found no signaling event curated by two databases is completely identical, and the average size of pathway components in PID is larger than that of Reactome.
In all, 108 associations related to 73 drugs are commonly confirmed by two databases, whose prediction scores are in the range of 0.95 1.00.
The cross-classification for the results of the condition by two databases and the formulas for calculating agreement statistics can be found in Additional file 1.
Briefly, the target mRNA should be differentially expressed, significantly anti-correlated with its miRNA regulator, and predicted by two databases, TargetScan and miRanda.
(Universal Protein Resource) UniProt (http://www.ebi.ac.uk/UniProt/), on its hand, is composed by two databases, Swiss-Prot and TrEMBL, which are curated and non-curated, respectively [ 42].
Variants were filtered by four databases, the 1000 Genomes Project, the HapMap database, the EVS database, and an in-house database from BGI, with the Minor Allele Frequency lower than 0.005.
In the flowering tissues of the closely related species Arabidopsis lyrata, the non-canonical expression of MIR319 was also supported by two databases [GEO GSE20442, GEO GSE20662] from two independent studies using SOLiD and Illumina Genome Analyzer respectively [ 26, 27].
