The influence of inorganic nitrogen compounds on gene expression profiles in neurospora crassa: a microarray analysis

Abstract

The purpose of this study was to investigate expression profiles of Neurospora crassa genes related to the nitrogen metabolism. Two nitrogen sources (ammonium and nitrate) and responses to light were meant to alter patterns of gene expression. The advent of full-genome microarrays enabled the measurement of mRNA levels in response to the environmental alterations. During the course of this experiment, and for all of the data sets discussed here, a total of 10526 ORFs based on MIPS or Broad Institute predictions had expression data. Further investigations involved recognizing the statistically different expressed genes. Two approaches were used for that purpose– filtering software of BRB-array tool, and arbitrary cut-off function of MatLab-script. The next step in the analysis was to find the patterns in gene expression by two clustering methods – hierarchical clustering and k-means clustering. The six clusters revealed by hierarchical clustering showed a great deal of overlap with the clusters recognized by kmeans clustering. The analysis of clusters involved visual investigation and functional prediction, which resulted in heat-maps, where one can connect the functions to a specific environmental condition. However, the majority of the statistically different expressed genes were not identified by functional prediction software. The genes related to a specific functional category were also investigated and results were compared to other studies.