基因表达差异显示实验

The systematic analysis of miRNA expression and its potential mRNA targets constitutes a basal objective in miRNA research in addition to miRNA gene detection and miRNA target prediction. In this chapter we address methodical issues of miRNA expression analysis using self-organizi ...

Inferring microRNA (miRNA) functions and activities has been extremely important to understand their system-level roles and the mechanisms behind the cellular behaviors of their target genes. This chapter first details methodologies necessary for prediction of function and a ...

Bioinformatics programs have helped tremendously in identifying the targets of microRNAs, which are small noncoding RNAs that regulate gene expression posttranscriptionally. However, the partial complementarity between miRNAs and their targets hinders the accuracy of t ...

Noncoding RNAs (ncRNAs) constitute an evolutionary conserved system involved in the regulation of biological functions at posttranscriptional level. The capability to rapidly adapt their metabolism is essential for the survival of organisms. NcRNAs are a valuable means used by c ...

MicroRNAs (miRNAs) are important players in gene regulation. The final and maybe the most important step in their regulatory pathway is the targeting. Targeting is the binding of the miRNA to the mature RNA via the RNA-induced silencing complex. Expression patterns of miRNAs are highly speci ...

In this review, current knowledge and ideas regarding several important functional-, structural-, and sequence-related aspects of microRNAs (miRNAs) are summarized. The current research on structural and functional aspects of miRNAs is rapidly growing, and new information app ...

MicroRNAs (miRNAs) are single-stranded, small, noncoding RNAs of about 22 nucleotides in length, which control gene expression at the posttranscriptional level through translational inhibition, degradation, adenylation, or destabilization of their target mRNAs. Althou ...

Zebrafish has become a widely used model for analysis of gene function. Several methods have been used to create mutations in this organism and thousands of mutant lines are available. However, all the conventional zebrafish mutations affect the gene in all cells at all time, making it difficult to ...

Endothelial cells are highly sensitive to high doses of ionizing radiation and the cellular response leads to acute damage of the endothelium. This chapter describes how to measure the effects of ionizing radiation on the proteome of endothelial cells, here showing analysis at 4 and 24 h after ex ...

When studying gene function in vivo during development, gene expression has to be controlled in a precise temporal and spatial manner. Technologies based on RNA interference (RNAi) are well suited for such studies, as they allow for the efficient silencing of a gene of interest. In contrast to cha ...

Embryonic stem cell (ESC) differentiation is a useful means by which to produce large quantities of cells in vitro representing early stages of embryonic development. A conditional gene expression system allows interrogation of factors at specific time points in the differentiation ...

RNA interference (RNAi) is an evolutionarily conserved mechanism of gene silencing induced by double-stranded RNAs (dsRNAs). Among the widely used dsRNAs, small interfering RNAs (siRNAs) and short hairpin RNAs have evolved as extremely powerful and the most popular gene silencing re ...

Antibodies are indispensable detection reagents for research and diagnostics and represent the biggest class of biological therapeutics on the market. In vitro antibody selection systems offer many advantages over animal-based technologies because the whole selection pro ...

Artificial nucleases have developed into powerful tools for introducing precise genome modifications in a wide variety of species. In this chapter the authors provide detailed protocols for rapidly constructing zinc finger nucleases (ZFNs) and TALE nucleases (TALENs) and evalu ...

Nontraditional model species need new tools for the functional testing of genes, both conserved and lineage-specific genes. These tools should enable the exploration of gene function, either via knock-downs of endogenous genes or via over-expression and ectopic expression of trans ...

DNA methylation, a DNA modification by adding methyl group to cytosine, has an important role in the regulation of gene expression. DNA methylation is known to be associated with gene transcription by interfering with DNA-binding proteins, such as transcription factors. DNA methylation ...

Cancer-specific High-throughput Annotation of Somatic Mutations (CHASM) is a computational method that uses supervised machine learning to prioritize somatic missense mutations detected in tumor sequencing studies. Missense mutations are a key mechanism by which importa ...

This chapter provides a description and illustration of CancerMutationAnalysis and Cancer MutationMCMC, two open source R packages specifically designed for the analysis of somatic mutations in cancer genome studies, at both the gene and gene-set levels.

Patterns in time-course gene expression data can represent the biological processes that are active over the measured time period. However, the orthogonality constraint in standard pattern-finding algorithms, including notably principal components analysis (PCA), confo ...

With the development of high-throughput gene expression profiling technologies came the opportunity to define genomic signatures predicting clinical condition or cancer patient outcome. However, such signatures show dependency on training set, lack of generalization, and ...