MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database

Abstract

MachiBase (http://machibase.gi.k.u-tokyo.ac.jp/) provides a comprehensive and freely accessible resource regarding Drosophila melanogaster 5'-end mRNA transcription at different developmental states, supporting studies on the variabilities of promoter transcriptional activities and gene-expression profiles in the fruitfly. The data were generated in conjunction with the recently developed high-throughput genome sequencer Illumina/Solexa using a newly developed 5'-end mRNA collection method.

Figure 1.

Statistical analysis of the TSS information. (A) A dot represents one non-redundant 5′-end tag, such that the values on the x-axis and y-axis indicate the frequencies of the focal tags in the respective experiments. (B) A case in which the known representative TSS is not consistent with the most frequent TSS. Note that the most abundant TSSs coincide across the seven different libraries. (C) The distribution of distances between the known representative TSSs and most frequent TSSs. Overall, 1033 (8.8%) of the 11 725 known representative TSSs coincide with the most frequent TSSs.

Figure 2.

Snapshot of the MachiBase genome browser. The frequencies of the 5′-end mRNA tags mapped to individual positions on the fruitfly genome in the seven libraries are displayed as histograms in the bottom seven tracks. In the histograms, the vertical bars in log scale indicate the numbers of 5′-end mRNA tags aligned to each position on the x-axis. The upper track shows the exon–intron structures of two alternative splice variants. Observe that the peaks for the 5′-end tags are around the 5′-end of the longer splice variant in all of the seven libraries. In addition, note that many 5′-end tags are expressed from the second, second-to-last, and last exons in four adult samples (young/old and male/female).