WGCNA determines pair-wise correlations between gene expression profiles to create modules (clusters) of co-expressed genes (Additional file 2: Figure S2).
A principal components analysis (affycoretools 1.30.0) was then conducted on voom-transformed values (limma 3.14.4) (Smyth 2004) of the differentially expressed isotigs/contigs to examine the overall correlations between gene expression profiles and their phenotype/dietary treatments.
The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance.
We present a methodology for understanding the relationship of gene expression and neuroanatomy based on correlation between gene expression profiles across tissue samples.
The case for direct interaction was bolstered by similarities between gene expression profiles of plants with various deficiencies in photoreceptors and COP1.
Pearson's correlation coefficient between gene expression profiles of recurrences of the same tumour ranged between 0.4191 and 0.8303 (median: 0.5492).
Note that at present there is no uniformly accepted, epistemologically pure meaning of 'distances' between gene expression profiles, and different metrics are useful in different situations.
If selection is acting on gene sequences to maximize expression efficiency, we might expect to find a relationship between gene expression profiles and some descriptions of sequence parameters.
They both measure the global similarity/divergence between gene expression profiles over multiple conditions/tissues, which may leave condition-specific / tissue-specific changes of gene expression undetected.
The method required a similarity measure to guide the search procedure and a Euclidean distance measure between gene expression profiles was adopted.
Although the comparison between gene expression profiles between LGMD2A with and without eosinophilia would be interesting, it was not possible to perform.
