基因表达差异显示实验

Information derived from genomic and post-genomic data can be efficiently used to link gene and function. Several web-based platforms have been developed to mine these types of data by integrating different tools. This method paper is designed to allow the user to navigate these platforms in o ...

Most high-throughput methods which are used in molecular biology generate gene lists. Interpreting large gene lists can reveal mechanistic insights and generate useful testable hypotheses. The process can be cumbersome and challenging. Multiple commercial and open solution cu ...

Functional genomics experiments and analyses give rise to large sets of results, each typically quantifying the relation of molecular entities including genes, gene products, polymorphisms, and other genomic features with biological characteristics or processes. There is tr ...

The abundance of publicly available life science databases offers a wealth of information that can support interpretation of experimentally derived data and greatly enhance hypothesis generation. Protein interaction and functional networks are not simply new renditions of e ...

The aim of this chapter is a step-by-step guide on how to infer gene networks from gene expression profiles. The definition of a gene network is given in Subheading 1, where the different types of networks are discussed. The chapter then guides the readers through a data-gathering process in order to bui ...

The determination of the function of the protein products of genes has been a major focus of molecular biology since the founding of the discipline. The development of knock-in, knock-down, and transgenic methodologies has greatly speeded laboratory discoveries, while the development ...

With the rise of tablets, truly portable molecular graphics are now available for wide use by scientists to share structural information in real time at a reasonable cost. We have surveyed the existing software available on Apple iPads and on Android tablets in order to make a recommendation to pot ...

Modeling and analogy are commonly used to identify the part that a metal may play in the structure or function of a new protein which has been recognized by structural genomics. Mespeus (http://mespeus.bch.ed.ac.uk/MESPEUS_10/) lists metal protein interactions whose geometry has been exp ...

iRefWeb is a bioinformatics resource that offers access to a large collection of data on protein–protein interactions in over a thousand organisms. This collection is consolidated from 14 major public databases that curate the scientific literature. The collection is enhanced with a r ...

Quality control of three-dimensional structures of macromolecules is a critical step to ensure the integrity of structural biology data, especially those produced by structural genomics centers. Whereas the Protein Data Bank (PDB) has proven to be a remarkable success overall, the in ...

Mass spectrometric analyses of proteins affinity-purified from cell lysates are routinely used by cell biologists to characterize the composition and the modifications of protein complexes. Here, we describe a protocol that combines affinity-purification with chemical cro ...

The recent innovation of collecting X-ray scattering from solutions containing purified macromolecules in high-throughput has yet to be truly exploited by the biological community. Yet, this capability is becoming critical given that the growth of sequence and genomics data is sign ...

There is increasing interest in applying NMR spectroscopy to the study of large protein assemblies. Development of methyl-specific labeling protocols combined with improved NMR spectroscopy enable nowadays studies of proteins complexes up to 1 MDa. For such large complexes, the maj ...

The success of homodimer structure determination by conventional solution NMR spectroscopy relies greatly on interchain distance restraints (less than 6 �) derived from nuclear Overhauser effects (NOEs) obtained from 13C-edited, 12C-filtered NOESY experiments. However, t ...

Diffraction anisotropy is characterized by variation in diffraction quality with reciprocal lattice direction. In the example presented here, diffraction extended to 2.1 � resolution along undefined and undefined directions but only to 3.0 � along the undefined direction. Severe anisotropy such as this is often as ...

The last years have seen a major development in automation for protein production, crystallization, and X-ray diffraction data collection, which has contributed to accelerate the pace of structure solution and to facilitate the study of ever more challenging targets through macromo ...

Construct design and sample formulation are critical in structural biology projects. Large numbers of sample variants are often produced and analyzed for a single target and significant effort is dedicated to sample characterization in order to identify at an early stage the most promi ...

Proteins naturally expressed in eukaryotic organisms often require host chaperones, binding partners, and posttranslational modifications for correct folding. Ideally the heterologous expression system chosen should be as similar to the natural host as possible. For examp ...

A powerful approach utilizing polyproteins for balancing stoichiometry of recombinant multiprotein complexes overproduced in baculovirus expression vector systems (BEVS) is described. This procedure has been implemented here in the MultiBac system but can also be directly ...

Current baculovirus expression vector systems (BEVS) rely on either using homologous recombination or site specific transposition (Tn7 transposition) to obtain recombinant baculovirus. Each approach has its own merits. To date, the choice of transfer plasmids limited expres ...