The influence of inorganic nitrogen compounds on gene expression profiles in neurospora crassa: a microarray analysis
Master thesis
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http://hdl.handle.net/11250/182620Utgivelsesdato
2014-02Metadata
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Sammendrag
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.
Beskrivelse
Master's thesis in Biological chemistry