Nevertheless, the proposed system is potentially useful in the modern era of integrating microarray data based upon the probe sequence alone.
To identify A. niger genes potentially involved in galacturonic acid catabolism, we have previously compared A. niger N402 microarray data obtained upon growth of the fungus on various carbon sources.
Microarray data exist upon stimulation with IL-17 for human vascular smooth muscle cells [ 14], bronchial epithel cells [ 5, 15], and upon TNF-α/IL-17 stimulation for the preosteoblast cell line MC3T-E1, ST2 and MEFs [ 12], human rheumatoid arthritis synoviocytes [ 13, 16], MEFs and HeLa cell lines [ 17].
Due to the resulting larger search space the methodology discussed here is likely to generate greater reshuffling in the results produced upon processing of microarray data from such more sophisticated organisms.
Differentially expressed genes (DEGs) upon EGF treatment were detected from microarray data with the RankProd algorithm [ 23] separately at the transcriptome and translatome level.
This study expands upon previous work on intensity-dependent variance estimation for microarray data by introducing a new metric, Imin, for pooling standard deviations.
Y.N. analyzed microarray data in the initial stage of this work, and N.H. and E.S. accomplished microarray data analyses.
We first analyzed the human microarray data for protein trafficking-related genes that were up-regulated in colon carcinoma Caco2 cells upon differentiation.
The source codes of the algorithms for preprocessing and statistical analysis of the microarray data are available upon request.
For example, our microarray data suggest that upon increased expression of MK5 L 337 A DAZAP2 becomes downregulated.
Based upon microarray data, we first evaluate the correlation between genes and the phenotype response.
