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Gene set enrichment analysis of neuroendocrine system of the silkworm Bombyx mori

Gabor Beke 1 ✉, Matej Stano 1, Ivana Daubnerova 2, Dusan Zitnan 2, Lubos Klucar 1

1Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia

2Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia

Beke G et al. (2015) EMBnet.journal 21(Suppl A), e829. http://dx.doi.org/10.14806/ej.21.A.829

Silkworm Bombyx mori represents a model organism for studying the neuroendocrine system in invertebrates. This system of nervous organs and endocrine glands regulates large number of life functions including movement, ecdysis, courting and mating. We have analysed strand-specific Illumina RNA-seq data from B. mori samples originated from different endocrine glands of both sexes and several developmental stages. Reads were mapped to the B. mori transcriptome using the Bowtie 2 aligner. Since the silkworm genome is abundant in repetitive sequences (Mita et al., 2004), the mapping allowing unlimited multi-mappings (required by eXpress) was extremly computing demanding. Transcript level RNA-seq quantification was performed using the eXpress tool based on an online expectation–maximization algorithm. Obtained data were consequently analysed in several gene set enrichment packages, including topGO and gplots (both R packages), where highly expressed genes were clustered and visualised, according to the functional GO enrichment analysis, and clustered by gene expression level.

Acknowledgements

The study is supported by the APVV-0827-11, VEGA 2/0164/15, IMTS 26230120002 and IMTS 26210120002 grants.

References

Mita K et al. (2004) The genome sequence of silkworm, Bombyx mori. DNA Res. 11(1), 27-35. http://dx.doi.org/10.1093/dnares/11.1.27

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