基因表达差异显示实验

RNA silencing, including RNA interference, is a novel method of gene regulation and one of the potent host-defense mechanisms against the viruses. In the course of evolution, the viruses have encoded proteins with the potential to suppress the host RNA silencing mechanism as a counterdefen ...

Social insects represent a group of organisms that have dual importance from perspectives relating to both basic and applied science. From a basic perspective, social insects serve as excellent model systems for studying social organization, behavioral ecology, neurobiology, and ...

The analysis of gene function during embryonic development asks for tight temporal control of gene expression. Classic genetic tools do not allow for this, as the absence of a gene during the early stages of development will preclude its functional analysis during later stages. In contrast, RN ...

With the recent advances in mouse genetics, it is now possible to mark specific cell types genetically in vivo and to study the fate of cells during development and adulthood. Cells are labeled and followed in vivo through the stable expression of reporter genes in particular cell types. The two most c ...

High-throughput experiments in biology often produce sets of genes of potential interests. Some of those gene sets might be of considerable size. Therefore, computer-assisted analysis is necessary for the biological interpretation of the gene sets, and for creating working hypothe ...

Expression data from knockout mutants is a powerful tool for gene function inference, permitting observation of the phenotype of a deleted gene on the organismal scale. A computational method is demonstrated herein to assess gene function from gene expression measured in deletion muta ...

Nonnegative matrix factorization is a machine learning algorithm that has extracted information from data in a number of fields, including imaging and spectral analysis, text mining, and microarray data analysis. One limitation with the method for linking genes through microarray d ...

Highly parallel gene-expression analysis has led to analysis of gene regulation, in particular coregulation, at a system level. Promoter analysis and interaction network toolset (PAINT) was developed to provide the biologist a computational tool to integrate functional genomi ...

The number of experimentally verified, intrinsically disordered (ID) proteins is rapidly rising. Research is often focused on a structural characterization of a given protein, looking for several key features. However, ID proteins with their dynamic structures that interconvert ...

Identification of coordinate gene expression changes across phenotypes or biological conditions is the basis of the ability to decode the role of gene expression regulatory networks. Statistically, the identification of these changes can be viewed as a search for groups (most typica ...

Multiple sequence alignment analysis is a powerful approach for translating the evolutionary selective power into phylogenetic relationships to localize functional coding and noncoding genomic elements. The tool Mulan (http://mulan.dcode.org/) has been designed to effec ...

Sequence alignment between remotely related proteins has been one of the more difficult problems in structural biology. Improvements have been achieved by incorporating information that enhances the diversity of the substitution matrices. NdPASA is a web-based server that opti ...

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between protein or nucleotide sequences. The program compares nucleotide or protein sequences to sequence in a database and calculates the statistical significance of the matches. This chapter first pr ...

We present a method to predict cis-acting elements for a given gene by detecting over-represented motifs in promoters of a set of ortholo gous genes in prokaryotes (single-gene, multiple-genomes approach). The method has been used successfully to detect regulatory elements at various ta ...

Discovery of transcription factor binding sites is a crucial and challenging problem in bioinformatics. Several computational tools have been developed for this problem, popularly known as the motif-finding problem. PhyME is an ab initio motif-finding algorithm, which finds over ...

Bioinformatic and experimental analyses of promoter regions are available for a long time. Finding of the transcription factor binding sites (TFBSs), however, by either method still faces a number of problems. For example, because of the ambiguity of binding of transcription factors, the ...

Here, we describe the usage of Fastcompare, a simple and efficient comparative approach for finding short noncoding DNA (e.g., transcription factor binding sites) and mRNA (e.g., microRNA target sites) sequences that are globally conserved between two genomes. Fastcompare is based on the ...

We present a method to predict cis-acting elements by detecting over-represented motifs in promoters of a set of coregulated genes (single-genome, multigenes approach). The method has been used successfully to detect regulating elements in bacteria and yeast. It can be used with higher or ...

Phylogenetic footprinting is powerful technique for finding functional elements from sequence data. Functional elements are thought to have greater sequence constraint than nonfunctional elements, and, thus, undergo a slower rate of sequence change through time. Phylogene ...

The Gibbs Motif Sampler (Gibbs) is a software package used to predict conserved elements in biopolymer sequences. Although the software can be used to locate conserved motifs in protein sequences, its most common use is the prediction of transcription factor binding sites (TFBSs) in promot ...