Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

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The Pfam protein families database

Background: Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader’s ability to evaluate critically the quality of the results presented or to repeat the experiments.

Content: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement.

Summary: Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.

/pdf/the-miqe-guidelines-minimum-information-for-publication-of-27m8n04lrd.pdf

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

http://science.sciencemag.org/content/sci/291/5507/1304.full.pdf

The sequence of the human genome.

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets

Shouldn't enantiomeric purity be included in the 'minimum information about a bioactive entity? Response from the MIABE group

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Shotgun proteomics experiments often provide a big amount of spectra data; however, a big part of them remain unidentified. Many unidentified spectra that are high probably from peptides could be revealed by data mining methods such as clustering. This idea motivates researchers to build 'spectral archives' to identify more peptides from the previously analysed resources. The objective is to build a general way to identify peptides for these high possibility spectra in spectral archives, to help biologists to get more output from the data. We here propose a novel generic pipeline for this approach, based on the PRIDE cluster resources, rather than building a complete archive from scratch. We applied our pipeline to test the identification of endogenous neuropeptides in rat. 33 high probability peptide-induced spectra have been exposed from rat's unidentified spectra in PRIDE cluster's archive.

A pipeline for identifying endogenous neuropeptides from spectral archives

We will provide an overview of recent developments in the tools and resources provided by the EBI Proteomics Services Team.

The IntAct molecular interaction database (http://www.ebi.ac.uk/intact)[1] now offers 163.000 curated binary molecular interactions. Using the Distributed Annotation System (DAS)[2] and DASTY (http://www.ebi.ac.uk/dasty), we are currently enhancing the IntAct molecular view through direct integration with external resources, in particular UniProt and ChEBI. We will provide a detailed view of the process and our experience using DAS for data integration and robust data maintenance.

The PRIDE proteomics identifications database (http://www.ebi.ac.uk/pride) [3] provides more than 500.000 protein identifications, supported by more than 3 million identified peptides. We will report on recent improvements to data submission system and interface, in particular the visualization of PRIDE peptides through DAS, as well as PRIDE protein sets on Reactome pathways.

A major challenge not only, but particularly in proteomics data resources is the efficient management of consistent protein identifiers and controlled vocabularies. We will describe two major tools to address these tasks, the PICR Protein Identifier Cross-Referencing service (http://www.ebi.ac.uk/Tools/picr), and the OLS Ontology Lookup Service (http://www.ebi.ac.uk/ols). PICR provides high quality mapping between protein identifier namespaces, based on a database of more than 15 million unique protein sequences and associated identifiers. OLS provides efficient access to currently almost 700.000 terms from 60 controlled vocabularies in OBO format. Both systems provide interactive as well as web service access, and are publicly available without restrictions.

EBI Proteomics Services

Protein-protein interaction networks provide insights into the relationships between the proteins of an organism thereby contributing to a better understanding of its cellular processes. Nevertheless, large-scale interaction networks are available for only a few model organisms. Thus, interologs are useful for a systematic transfer of protein-protein interactions to other organisms. In this study, we developed two methods based on the interolog concept and constructed a new network of 8,783 interactions for Synechocystis. Furthermore, we developed an automatic tool to predict protein-protein interactions for all species with a sequenced genome. This open-source tool is available at http://biodev.extra.cea.fr/interoporc.

Henning Hermjakob

Papers

Shouldn't enantiomeric purity be included in the 'minimum information about a bioactive entity? Response from the MIABE group

A pipeline for identifying endogenous neuropeptides from spectral archives

EBI Proteomics Services

Inference of Synechocystis protein interaction network

BioModels Database: a public repository for sharing models of biological processes.