基因表达差异显示实验

This chapter outlines a typical workflow for micraorray data analysis. It aims at explaining the background of the methods as this is necessary for deciding upon a specific numerical method to use and for understanding and interpreting the outcomes of the analyses. We focus on error handling, v ...

DNA duplex stability on oligonucleotide microarray was calculated using recently developed electrostatic theory of on-array hybridization thermodynamics. In this method, the first step is to finding the enthalpy and entropy of duplex formation in solution. This standard calcu ...

The human genome project has opened up a new page in scientific history. To this end, a variety of techniques such as microarray has evolved to monitor the transcript abundance for all of the organism’s genes rapidly and efficiently. Behind the massive numbers produced by these techniques, which a ...

A method for systematically selecting the large number of sequences needed to custom design an oligonucleotide microarray was presented. This approach uses a Perl script to query sequence databases with gene lists obtained from previously designed (and publicly available) microa ...

The complexity of workflows for the production of high quality microarrays asks for the careful evaluation and implementation of materials and methods. As a cornerstone of the whole microarray process, the microarray substrate has to be chosen appropriately and a number of crucial consi ...

Gene expression microarrays are becoming increasingly widespread, especially as a way to rapidly identify putative functions of unknown genes. Accurate microarray data analysis, however, still remains a challenge. The recent availability of multiple types of high-throughput ...

As the performance of microarray experiments is directly dependent on the quality of the materials, the suitability of the protocols, and the accuracy of the work performed, optimization of existing microarray workflows is needed in almost every experiment to achieve higher quality and ...

A move away from high-density screening array formats and the implementation of probes specifically identifying targets for application in low-density hybridization capture analyses is growing in importance. Some of the highest specificity for bioassays that encompasses use ...

Based on the selection of a suitable surface chemistry and bearing the option for optimization using a defined workflow, standard experimental protocols for the processing of microarrays can be used as starting points for a successful experiment. In Chapters 2 and 3, general quality consi ...

With the completion of the Human Genome Project, the microarray technology has evolved into a sophisticated platform by which complex diseases such as cancer, can be studied at the genome, transcriptome, and proteome levels. Here, various microarray platforms, namely comparative gen ...

Microarrays are a powerful laboratory tool for the simultaneous assessment of the activity of thousands genes. Remarkable advances in biological sample collection, preparation and automation of hybridization have enabled the application of microarray technology to large, p ...

The last decade has witnessed an impressive upsurge in the utilization of microarray platforms for biomedical research. However, the application of this emerging technology in medical practice lagged behind. This lag is understandable because there are specific issues pertaini ...

The microRNAs (or miRNAs) are small noncoding RNAs (21—25 nt) that are processed from large hairpin RNA precursors and are believed to be involved in a wide range of developmental and cellular processes, by either repressing translation or triggering mRNA interference (RNA interference). ...

OLIGO performs a range of functions for researches in PCR and related technologies such as PCR and sequencing primer selection, hybridization probe design, inverse and real-time PCR, analysis of false priming using a unique priming efficiency (PE) algorithm, design of consensus and mult ...

The physical principles of DNA hybridization and folding are described within the context of how they are important for designing optimal PCRs. The multi-state equilibrium model for computing the concentrations of competing unimolecular and bimolecular species is described. Se ...

The conflicts between several design objectives for PCR primers are computationally resolved by specifying a set of ideal parameters and searching for primer pairs whose parameters approximate this ideal point as close as possible. It thus becomes feasible to identify an “optimum” and to ...

Primer extension by thermostable DNA polymerase in PCR starts from the 3′-end of a primer. If the PCR starting process fails, the entire PCR fails. Primer sequences at the 3′-end often interfere with success in PCR experiments. Over 2000 primer sequences from successful PCR experiments used with v ...

This chapter describes the statistical method that can be used to predict the success and failure of a designed primer based on properties of genomic sequence surrounding the primer extension, using user's own existing genotyping database. After scores that measure properties of genom ...

I describe the approaches for choosing primer parameters and calculating primer properties to build a statistical model for PCR primer design. Statistical modeling allows you to fine-tune the PCR primer design for your standard PCR conditions. It is most appropriate for the large organi ...

The profiling of mRNA expression based on DNA arrays has become a powerful tool to study genome-wide transcription of genes in a number of organisms. GST-PRIME is a software package created to facilitate large-scale primer design for the amplification of probes to be immobilized on arrays for tr ...