A microarray dataset comparing the response of seven Arabidopsis accessions, Col-0, Cvi-1, Est, Kin-0, Mt-0, Tsu-1 and Van-0, to exogenous salicylic acid treatment was utilized to directly assess the impact of gene duplication on different sources of gene expression variation [40].
Just two genes manifested a statistically significant opposite direction of differential expression in the MTP-microarray dataset compared to both the oligo-dT dataset and the independent RNA-Seq datasets (YDR179W-A, YKL203C).
We reviewed Oncomine [ 29, 30] for independent human breast cancer microarray datasets comparing estrogen receptor (ER -negative and ER -negativetumors.
We searched the public cancer microarray database, Oncomine [ 9], to identify expression microarray datasets that compared the expression of primary tumors versus distant metastases of various cancer types.
The Ved and PS microarray datasets were compared using the Significance Analysis of Microarrays (SAM) tool in the TM4 software package [ 66] and differentially expressed genes are listed in Additional file 11: Table S8.
We apply our techniques to publicly available microarray datasets and compare our results with findings discussed in [36].
The gene targets of highly expressed miRNAs on aggregate tend to display a lower overall expression [23], [33], which can be detected in microarray datasets by comparing their expression levels of target vs. non-target mRNAs with a Wilcoxon rank-sum test [34].
Also, we explored BLBC and TNBC in two large microarray datasets by comparing the expression levels of the five markers according to the subtypes.
Specifically, we first propose a simple F-test-based procedure for identifying DV genes from large microarray datasets, and compare our method with a number of more robust variants using simulated data (here 'robust' is used to mean resistant to the effect of outliers).
Here we used publicly accessible microarray datasets to compare, in a series of HELUs from noncancerous adult breasts and corresponding patient-matched, normal TDLUs, the expression pattern of genes experimentally recognized to be involved in regulating cell identity and mammary gland remodeling.
For the analysis of the X microarray dataset only, we compared the wrapper approaches RFs, recursive feature elimination (RFE; Guyon et al., 2002) and nearest shrunken centroids (NSCs; Tibshirani et al., 2002).
