Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
RobiNA is an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface and supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state of the art biostatistical methods developed in the R/Bioconductor projects.
New developments are presented, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, and extensions of the software to incorporate more biological information including visualization of coresponding genes and horizontal searches for similar global responses across large numbers of arrays.
These analyses illustrate how MapMan can be used to analyse and compare global transcriptional responses between phylogenetically distant species, and show that analyses at the level of functional categories are especially useful in cross-species comparisons.
PageMan is introduced, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies, enabling researchers to gain a rapid overview of the biological responses in the experiments.
Differentially expressed and highly P-specific putative regulator genes were identified that presumably play central roles in coordinating the complex responses of plants to changes in P nutrition.
It is confirmed that sugar and circadian regulation are the major inputs in Col-0 but that sugars dominate the response in pgm, and a set of candidate regulatory genes are identified that show robust responses to alterations in sugar levels and change markedly during the diurnal cycle.
The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences using the MapMan 'BIN' ontology, which is tailored for functional annotation of plant 'omics' data.
Examples from the literature, wherein co-expression has been used to corroborate and discover various aspects of plant biology are presented, and statistical issues including how normalization of gene expression data can influence co- expression results are discussed.
GD, The Golm Metabolome Database is presented, an open access metabolome database, which provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools, e.g. with regard to methods, spectral information or compounds.