Effects of T-stackprobes On Affymetrix human genechip® data

The Karst Hoogsteen theory, that bases can also pair up in many different ways, opens up another door of research for scientists. It is found that nucleotide sequences having continuous guanines (G-stack probes) form unusual structures called G-Quadruplex structures due to guanine-guanine (G-G) bindings. Researchers have found that some abnormal behaviors are seen on microarray particularly on Affymetrix GeneChip® and they associated these abnormal behaviors with the formation of G-quadruplex structures due to the presence of G-stack probes. Hence, G-stack probes were suggested unreliable for gene expression measurement. This left another question that if G-G can affect GeneChip® then interaction among other bases like A-A, T-T and C-C may also be problematic for GeneChips®. The main objective of this research is to analyze the effects of T-T binding at probe level data of Affymetrix GeneChip®. Data of HG_U95C GeneChip® designed for Homo Sapiens (Human) is downloaded from NCBI-GEO repository. The abnormal behavior of G-stack probes was shown as the G-stack probes were not correlated with their other member probes while they were correlated with each other regardless of their genes/probe sets. Similarly, the correlation among the T-stack probes is calculated to verify if they are behaving like G-stack probes. The results suggest that thymine-thymine binding does not affect the human chip. Hence it is all fine if T-stack probes are present on any GeneChip® design.