Analyses

This Analysis reports the development and assessment of 645 multiple reaction monitoring (MRM) mass spectrometry assays to quantify 319 targeted human breast cancer proteins. The results of this pilot project coordinated among three individual groups suggest that an organized international effort to generate MRM assays to the human proteome will be possible.

The RGASP consortium compared 25 RNA-seq analysis programs in their ability to identify exons, reconstruct transcripts and quantify expression levels. Assembly of isoforms and their expression levels in higher eukaryotes remains a challenge.

Authors compare RNA-seq aligners on mouse and human data sets using benchmarks such as alignment yield, splice junction accuracy and suitability for transcript reconstruction. The work highlights the strength of each program and discusses outstanding needs in RNA-seq analysis.

A systematic evaluation of various single-cell RNA-seq approaches reports their sensitivity, accuracy and reproducibility and establishes the high performance of a high-throughput microfluidic method.

This comparison of five RNA-seq library preparation methods highlights metrics for assessing the suitability of the methods for samples with low amounts of RNA and/or those with low-quality RNA.

A systematic study of the intra- and interlaboratory reproducibility of a standardized affinity purification–mass spectrometry protocol demonstrates the high reproducibility of this technique and hints at the feasibility of a large-scale human interactome project through interlaboratory efforts.

In this analysis, the authors directly compared immunofluorescence and fluorescent-protein tagging of 506 human proteins and studied their subcellular localization. They conclude that the two methodologies are highly complementary and propose an integrative strategy for the characterization of newly identified proteins.

In this analysis, the authors directly compared the performance of flow cytometry data processing algorithms to manual gating approaches. The results offer information of practical utility about the performance of the algorithms as applied to different data sets and challenges.

A report on the results of the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment.

This analysis comprehensively compares methods for gene regulatory network inference submitted through the DREAM5 challenge. It demonstrates that integration of predictions from multiple methods shows the most robust performance across data sets.

Algorithms that integrate genome-wide copy number and gene expression data offer a promising way to uncover genes that drive the progression of cancers. The performance of ten software tools on simulated and real cancer datasets of different sizes is directly compared in this Analysis.

In this Analysis, the authors directly experimentally compare microbial opsins used for the control of neural activity. They extract essential principles and key parameters that can help end users with the design and interpretation of optogenetic experiments and guide tool developers in the characterization of future tools.

A quantitative characterization of the switching properties of 26 organic dyes relates these properties to the quality of localization-based super-resolution images they generate. The data are a useful resource for selecting dyes and point to avenues for future analysis.

A multilaboratory pilot project demonstrates that hybridoma and phage display technologies can be applied to produce high-affinity, high-specificity renewable antibodies to a set of 20 human SH2 domain proteins in a reasonable time frame, suggesting that a systematic, large-scale effort to generate renewable protein binders will be feasible.

The comparison of cross-linking and immunoprecipitation (CLIP) and photoactivatable ribonucleoside–enhanced CLIP (PAR-CLIP) protocols shows specific biases of each method in enriching subsets of binding sites of RNA-binding proteins and shows ways around these biases.

Compared in this Analysis are two widely used procedures for ribosomal RNA removal in metatranscriptomic samples, and the authors present recommendations to prevent misleading analyses of microbial communities.

A comparison of ordination analysis methods used to reveal gradients or clusters in sequence data from microbial communities reveals which methods are best suited for which community structure at different sequencing depth.

The authors compare quality metrics of libraries from seven strand-specific RNA-seq methods in terms of complexity, strand specificity, evenness and continuity of coverage, and expression profiling. They provide a computational pipeline to compare these metrics from any RNA-seq protocol.

A multilaboratory analysis characterized the ability of 27 different labs to identify 20 proteins at equimolar concentrations in a highly purified test sample mixture using mass spectrometry. The results show that while the technology is reproducible, many common experimental problems arise, and improved search engines and databases are still needed.

Different experimental designs for protein interaction mapping are modeled to compare their efficiency in completing an interactome map. Testing of the strategy that minimized the final experimental cost in an ongoing Drosophila melanogaster interactome project found 450 high-confidence interactions using only 47 microtiter plates.