As part of the EUROFAN Transcript Consortium, northern analysis was used to study the expression of 200 yeast orphan genes. Five transient growth conditions were analysed, including glucose upshift, stationary phase, nitrogen starvation, osmotic shock, and heat shock. Around 72% of the genes analysed were expressed at low level, about 12% were expressed at a medium level, and 3.5% at a high level relative to the ACT1 mRNA. Almost half of the genes were regulated significantly in response to at least one of the growth conditions. Expression levels did not correlate with the Codon Adaptation Index. These data were in accordance with the overall data set on 1000 novel ORFs produced by the Transcript Consortium as a whole. Second, transcript profiling was used to analyse global gene expression patterns during two types of filamentous growth in yeast: (a) the pseudohyphal growth of fus3 cells following nitrogen limitation on solid medium, and (b) the filamentous growth of haploid cells in response to isoamyl alcohol. In both cases, subsets of regulated genes were identified. Genes shown previously to be involved in filamentous growth, including CLN1, PGU1 and YLR042c, were also up-regulated during fus3-induced pseudohyphal growth. Genes sensitive to nitrogen catabolite repression were down-regulated in response to both fus3 and isoamyl alcohol-induced filamentation. In contrast, Gcn4p- and Pdr1p-regulated genes appeared to be significantly up-regulated in response to isoamyl alcohol. Therefore, yeast cells might sense this fusel alcohol as a toxic compound, thereby inducing a mechanism to export the compound from the cells.