Table 1.
Detailed statistics of microRNA data, which includes a total of 34,612 mature sequences, 28,421 stem-loop precursor sequences, 194 species and 5 kingdoms.
Fig 1.
Length distribution of mature miRNA sequences in 5 kingdoms (A) and schematic plot shows statistics of the cross-species sequence comparison (B).
(A) Length distribution of mature miRNA sequences in Animalia (red), Fungi (brown), Plantae (green), Protista (blue) and Viruses (purple) in both histogram (left) and Boxplots (right). (B) Schematic plot shows statistics of the cross-species sequence comparison. Within each species, light blue indicates the percentage of miRNAs that have homologues miRNA in Human, light purple represents the percentage of miRNAs that have homologues in other species within the same kingdom, and gray shows the percentage of miRNAs that have no homologues in any other species.
Fig 2.
Phylogenetic tree of miR-190/171 family and sequence alignments of hsa-miR-190a/b and sly-MIR171a.
(A) Phylogenetic tree of miR-190/171 family based on the 162 precursor sequences from 89 species, where three major clusters are formed for miR-190a, miR-190b, and miR-171. (B) Alignments among precursor sequences of hsa-miR-190a/b and sly-MIR171a. Hsa-miR-190b show sequence identify of 79% (with blast similarity score = 28.3, E-value = 2E-05) and 77% (with blast similarity score = 76.1, E-value = 2E-18) with sly-miR-171a (tomato) and miR-190a (human), respectively.
Table 2.
Performance summary for kingdom-wise classification and human secreted miRNA prediction.
Table 3.
Examples of overlapped discriminative features chosen by three kingdom-wise classifications and the human blood secretory prediction.
Table 4.
221 features that have been selected for the final ranking of possible circulating miRNAs, which are categorized into eight groups according to the feature type and involved sequence type.
Table 5.
Statistics of the top miRNA entries in the ranking list with respect to their origins.
Table 6.
Gene targets and functional analysis of the three top predictions of the transportable miRNAs in cow’s milk, EBV, and rLCV.
Fig 3.
The multiple sequences alignment among the binding regions of 15 miR-487b targets in cow (_bta) and 46 targets in human (_hsa).
Fig 4.
Regulatory network of bta-miR-487b in human.
Blue octagon nodes indicate genes that are involved in MAPK signaling pathway (adjusted fisher test p-value = 0.034); purple circle nodes indicate genes that are involved in regulation of actin cytoskeleton (p-value = 0.042); green triangle nodes represent genes that are involved in axon guidance (p-value = 0.042); pink square nodes denote genes that are involved in butanoate metabolism (p-value = 0.052). All light blue small circle nodes represent other predicted targets of miR-487b.