Figure 1.
Flow chart of processing stages involved in establishing signatures from RNA-Seq and Microarray analysis for connectivity mapping.
Figure 2.
sscMap output for the signature from the RNA-Seq dataset.
Figure demonstrates the volcano plot of the distribution of candidate compounds that may enhance (right side) or suppress (left side) the phenotype. Significant candidates are above the green line.
Table 1.
DESeq top ranking differentially expressed genes.
Table 2.
EdgeR top ranking differentially expressed genes.
Table 3.
The gene signature from the NGS dataset using DESeq analysis and their positions in the microarray DEGs by SamR.
Figure 3.
NGS signature genes explored in Microarray study.
The set of genes utilised in the NGS gene signature for sscMap are explored in the GEO Dataset Browser with the Wang et al microarray dataset.
Figure 4.
sscMap output for the signature from the Microarray dataset.
Distribution of candidate compounds that may enhance (right side) or suppress (left side) the phenotype of the Microarray study.
Table 4.
The gene signature from the microarray dataset using SamR analysis.
Table 5.
Compounds declared significant between both technologies that had full perturbation stability.
Table 6.
GeneCodis analysis with twenty-two sets of processes that were significantly enriched.
Figure 5.
Cotinine was the top candidate compound to suppress the proliferative phenotype.
Validation of cotinine as the top candidate to suppress cell proliferation phenotype induced via androgen pathway. A, Cells in 6 well plate format were treated with vehicle or various doses of cotinine for 96 hours. Total viable cell numbers were counted by haemocytometer. Cell counts are represented as relative to the untreated control value. B, Cells were treated with indicated doses of cotinine and seeded in xCELLigence 16 well E-plates. Real-time analysis of cell doubling rates was recorded and rate of doubling between 72–96 hours was plotted relative to untreated control using the system software. The experiment was repeated three times with similar results. ** denotes using unpaired two-tailed t-test.