Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila

Additional file 4:

The list of the 59 reference miRNAs identified by cloning. Table S1. The list of the 59 reference miRNAs. All the entries are clustered according to miRNA family information. The number of homologies in six flies, the results of different motif finding methods and the results of mature miRNA identification are presented in the file.

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Additional file 1:

The distributions of conservation ratios and the counts in Dme-Dps pair. Figure S1. The distributions are computed and plotted for three dataset: reference seed matches, shuffled seed matches and all 7-mers. A) The distribution of conservation ratios. B) The distribution of counts in Dme 3'-UTRs. C) The distribution of counts in Dme-Dps conserved 3'-UTRs.

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Additional file 2:

The histograms of PCSs and the trends of PCSs along the phyla. Figure S2. A)-G) The PCSs of all 7-mers, from left to right: the average PCSs and the PCSs in Dme-Dsi, Dme-Dya, Dme-Dan, Dme-Dps, Dme-Dmo, Dme-Dvi. The top panel of each sub-figure shows the histograms of the PCSs of all the 7-mers and the bottom panel shows the enlarged visions. H) The trends of the PCSs of 86 seed matches along the phyla. Because the evolutionary distances of the Dme-Dmo and Dme-Dvi pairs are the same, only the PCSs of the Dme-Dmo pairs are displayed.

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Additional file 3:

The histograms of conservation ratios along the phyla. Figure S3. A)-F) The conservation ratios of all 7-mers, from left to right: the conservation ratios in Dme-Dsi, Dme-Dya, Dme-Dan, Dme-Dps, Dme-Dmo, Dme-Dvi. The top panel of each sub-figure shows the histograms of the conservation ratios of all the 7-mers and the bottom panel shows the enlarged visions.

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Additional file 5:

The list of PCSs, counts and conservation ratios of all 7-mers. Table S2. The list of the all 16,384 7-mers. The "Type" column describes whether a 7-mer is derived the 5'-end of cloned/northern blotting/homology miRNAs or predicted miRNA candidates. The "Class" column describes whether a 7-mer is classified as positive by Cons-SVM. The "PCS:XX" columns present the pairwise conservation scores in "XX" condition. The "BC:X" columns present the counts in single "X" 3'-UTRs. The "AC:XX" columns present the counts in "XX" conserved 3'-UTRs. The "CR:XX" columns present the conservation ratios in "XX" pair.

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Additional file 6:

The list of the 78 pre-miRNAs in miRBase and related annotations. Table S3. The annotations of 78 pre-miRNAs and corresponding mature miRNAs.

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Additional file 7:

The list of the 41 predicted pre-miRNAs using RNAmicro. Table S4. The annotations of 41 pre-miRNAs such as corresponding mature parts, genomic location, homologies, etc.

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Additional file 8:

The target and anti-target GO categories of miRNAs. Table S5. The raw p-values and Bonferroni corrected p-values are reported for each GO category. The "Known_XX" columns are the p-values calculated for the 59 reference miRNAs. The "New_XX" columns are the p-values calculated for the 47 miRNA candidates. The "Cons_XX" columns are the p-values calculated for the 9 miRNA candidates with additional conservation in mosquito or honeybee.

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