| Summary: | <i>Aspergillus</i> spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating <i>A. fumigatus</i> and <i>A. niger</i> conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between <i>A. niger</i> and <i>A. fumigatus</i> during conidial germination. Specifically, the <i>turquoise</i> module was enriched with secondary metabolism, the <i>black</i> module was highly enriched with protein synthesis, the <i>darkgreen</i> module was enriched with protein fate, and the <i>blue</i> module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the <i>blue</i> module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in <i>A. fumigatus</i> and <i>A. niger</i>, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by <i>A. fumigatus</i> and <i>A. niger</i>, which underscores the potential of this approach.
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