Theoretically modeling microarray with the chemical equilibrium and thermodynamics

To date, the idea that microarray may shed the light on cellular processes by identifying groups of genes that appear to be co-expressed seems to remain a dream. This is partly because that there are some blank (meaning the knowledge is unavailable) or even erroneous areas in the fundamental theory in this field. This paper attempts to present the digest of microarray hybridization system with chemical thermodynamics, theoretically clarifying some misunderstandings and looking for answers to some critical questions around this technology, such as the mechanisms and conditions of quantitative measuring by hybridization reaction, the reasons of inconsistency of the data and the analysis results and the solutions, how to analyze the data, etc. A theoretical model for the next generation of microarray is proposed. We believe that this model is universal, laying the foundation for microarray technology from array design through the data analysis.