Analysis and visualization of tree space

We explored the use of multidimensional scaling (MDS) of tree-to-tree pairwise distances to visualize the relationships among sets of phylogenetic trees. We found the technique to be useful for exploring "tree islands" (sets of topologically related trees among larger sets of near-optimal trees), for comparing sets of trees obtained from bootstrapping and Bayesian sampling, for comparing trees obtained from the analysis of several different genes, and for comparing multiple Bayesian analyses. The technique was also useful as a teaching aid for illustrating the progress of a Bayesian analysis and as an exploratory tool for examining large sets of phylogenetic trees. We also identified some limitations to the method, including distortions of the multidimensional tree space into two dimensions through the MDS technique, and the definition of the MDS-defined space based on a limited sample of trees. Nonetheless, the technique is a useful approach for the analysis of large sets of phylogenetic trees.     

TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities

We describe a general multiplatform exploratory tool called TreeQ-Vista, designed for presenting functional annotations in a phylogenetic context. Traits, such as phenotypic and genomic properties, are interactively queried from a user-provided relational database with a user-friendly interface which provides a set of tools for users with or without SQL knowledge. The query results are projected onto a phylogenetic tree and can be displayed in multiple color groups. A rich set of browsing, grouping and query tools are provided to facilitate trait exploration, comparison and analysis. AVAILABILITY: The program, detailed tutorial and examples are available online (http:/genome.lbl.gov/vista/TreeQVista).     

SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data

SNP Chart is a Java application for the visualization and interpretation of microarray genotyping data primarily derived from arrayed primer extension-based chemistries. Spot intensity output files from microarray analysis tools are imported into SNP Chart, together with a multi-channel TIFF image of the original array experiment and a list of the actual single nucleotide polymorphisms (SNPs) being tested. Data from different and/or replicate probes that interrogate the same SNP, but that are scattered across the array grid, can be reassembled into a single chart format, specific for the SNP. This allows a quick and very effective 'visualization'/'quality control' of the data from multiple probes for the same SNP that can be easily interpreted and manually scored as a genotype. AVAILABILITY: http://www.snpchart.ca.     

Estimation and visualization of identity-by-descent within pedigrees simplifies interpretation of complex trait analysis

Linkage analysis identifies markers that appear to be co-inherited with a trait within pedigrees. The inheritance of a chromosomal segment may be probabilistically reconstructed, with missing data complicating inference. Inheritance patterns are further obscured in the analysis of complex traits, where variants in one or more genes may contribute to phenotypic variation within a pedigree. In this case, determining which relatives share a trait variant is not simple. We describe how to represent these patterns of inheritance for marker loci. We summarize how to sample patterns of inheritance consistent with genotypic and pedigree data using gl_auto, available in MORGAN v3.0. We describe identification of classes of equivalent inheritance patterns with the program IBDgraph. We finally provide an example of how these programs may be used to simplify interpretation of linkage analysis of complex traits in general pedigrees. We borrow information across loci in a parametric linkage analysis of a large pedigree. We explore the contribution of each equivalence class to a linkage signal, illustrate estimated patterns of identity-by-descent sharing, and identify a haplotype tagging the chromosomal segment driving the linkage signal. Haplotype carriers are more likely to share the linked trait variant, and can be prioritized for subsequent DNA sequencing.     

SNARE Dance: A musical interpretation of Atg9 transport to the tubulovesicular cluster

There is little doubt that humans rely on vision as their primary sensory input. However, various studies indicate that audiovisual combinations of data presentation actually enhance the ability of the learner to comprehend the information. We present an example of a musical-biological interface that provides an audible demonstration of SNARE protein function in the process of macroautophagy.     

WebGimm: An integrated web-based platform for cluster analysis,functional analysis,and interactive visualization of results

Cluster analysis methods have been extensively researched, but the adoption of new methods is often hindered by technical barriers in their implementation and use. WebGimm is a free cluster analysis web-service, and an open source general purpose clustering web-server infrastructure designed to facilitate easy deployment of integrated cluster analysis servers based on clustering and functional annotation algorithms implemented in R. Integrated functional analyses and interactive browsing of both, clustering structure and functional annotations provides a complete analytical environment for cluster analysis and interpretation of results. The Java Web Start client-based interface is modeled after the familiar cluster/treeview packages making its use intuitive to a wide array of biomedical researchers. For biomedical researchers, WebGimm provides an avenue to access state of the art clustering procedures. For Bioinformatics methods developers, WebGimm offers a convenient avenue to deploy their newly developed clustering methods. WebGimm server, software and manuals can be freely accessed at .     

Selection of informative clusters from hierarchical cluster tree with gene classes

Background  

A common clustering method in the analysis of gene expression data has been hierarchical clustering. Usually the analysis involves selection of clusters by cutting the tree at a suitable level and/or analysis of a sorted gene list that is obtained with the tree. Cutting of the hierarchical tree requires the selection of a suitable level and it results in the loss of information on the other level. Sorted gene lists depend on the sorting method of the joined clusters. Author proposes that the clusters should be selected using the gene classifications.     

Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R

SUMMARY: Hierarchical clustering is a widely used method for detecting clusters in genomic data. Clusters are defined by cutting branches off the dendrogram. A common but inflexible method uses a constant height cutoff value; this method exhibits suboptimal performance on complicated dendrograms. We present the Dynamic Tree Cut R package that implements novel dynamic branch cutting methods for detecting clusters in a dendrogram depending on their shape. Compared to the constant height cutoff method, our techniques offer the following advantages: (1) they are capable of identifying nested clusters; (2) they are flexible-cluster shape parameters can be tuned to suit the application at hand; (3) they are suitable for automation; and (4) they can optionally combine the advantages of hierarchical clustering and partitioning around medoids, giving better detection of outliers. We illustrate the use of these methods by applying them to protein-protein interaction network data and to a simulated gene expression data set. AVAILABILITY: The Dynamic Tree Cut method is implemented in an R package available at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting.     

Phenetic similarity among Dioscorea cayenensis cultivars as estimated by cluster analysis and minimum spanning tree

Two numerical taxonomic methods, cluster analysis and minimum spanning tree, were applied to classify 20 Nigerian cultivars of yellow yam (Dioscorea cayenensis). Cultivars were grown for 3 yr and 49 plant characters observed. The results were summarised as a dendrogram and an undirected minimum spanning tree. The classifications from both methods were complementary and facilitated a better understanding of the phenetic similarity between cultivars. Four main clusters were revealed with different intra-cluster variation. The clustering pattern was not remarkably affected by the two classificatory methods employed.     

Spatial autocorrelation and the interpretation of patterns of tree seed and seedling predation by rodents in old-fields

Spatial autocorrelation is ubiquitous in ecological systems. However, consideration of this phenomenon in seed and seedling predation studies has been limited, perhaps explaining some of the variation observed between studies and the difficulty in generalizing about the impacts of herbivores on successional processes. I examined the prevalence and patterns of spatial autocorrelation in seed and seedling survival between neighboring tree propagules in old-fields. All experiments were conducted within enclosures in which I manipulated the density of meadow voles ( Microtus pennsylvanicus ). Voles, and competitively inferior white-footed mice ( Peromyscus leucopus ), are the dominant consumers of tree seedlings and seeds in old-fields in the northeastern United States, respectively. An intermediate level of spatial autocorrelation was present in seed and seedling predation trials. Furthermore, the frequency of spatial autocorrelation increased under low-vole density conditions and in study sites with greater heterogeneity in vegetation cover. Survival of neighboring tree propagules was generally positively autocorrelated, suggesting that foraging by mice and voles contributes to a clumped pattern of tree propagule establishment in old-fields. A review of published predation studies found that only 8.3% attempted to test for spatial autocorrelation and that the minimum average spacing used between replicates is well below the average autocorrelation distance of 8.1±6.3 m observed in the current study. Patterns of autocorrelation appear somewhat predictable based on knowledge of the ecology of mice and voles and to provide insights into the factors influencing their foraging behavior and potential impacts on old-field succession.     

Artemis: sequence visualization and annotation

SUMMARY: Artemis is a DNA sequence visualization and annotation tool that allows the results of any analysis or sets of analyses to be viewed in the context of the sequence and its six-frame translation. Artemis is especially useful in analysing the compact genomes of bacteria, archaea and lower eukaryotes, and will cope with sequences of any size from small genes to whole genomes. It is implemented in Java, and can be run on any suitable platform. Sequences and annotation can be read and written directly in EMBL, GenBank and GFF format. AVAILABITLTY: Artemis is available under the GNU General Public License from http://www.sanger.ac.uk/Software/Artemis     

Genomorama: genome visualization and analysis

Background  

The ability to visualize genomic features and design experimental assays that can target specific regions of a genome is essential for modern biology. To assist in these tasks, we present Genomorama, a software program for interactively displaying multiple genomes and identifying potential DNA hybridization sites for assay design.     

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications

MOTIVATION: Tandem mass spectrometry combined with sequence database searching is one of the most powerful tools for protein identification. As thousands of spectra are generated by a mass spectrometer in one hour, the speed of database searching is critical, especially when searching against a large sequence database, or when the peptide is generated by some unknown or non-specific enzyme, even or when the target peptides have post-translational modifications (PTM). In practice, about 70-90% of the spectra have no match in the database. Many believe that a significant portion of them are due to peptides of non-specific digestions by unknown enzymes or amino acid modifications. In another case, scientists may choose to use some non-specific enzymes such as pepsin or thermolysin for proteolysis in proteomic study, in that not all proteins are amenable to be digested by some site-specific enzymes, and furthermore many digested peptides may not fall within the rang of molecular weight suitable for mass spectrometry analysis. Interpreting mass spectra of these kinds will cost a lot of computational time of database search engines. OVERVIEW: The present study was designed to speed up the database searching process for both cases. More specifically speaking, we employed an approach combining suffix tree data structure and spectrum graph. The suffix tree is used to preprocess the protein sequence database, while the spectrum graph is used to preprocess the tandem mass spectrum. We then search the suffix tree against the spectrum graph for candidate peptides. We design an efficient algorithm to compute a matching threshold with some statistical significance level, e.g. p = 0.01, for each spectrum, and use it to select candidate peptides. Then we rank these peptides using a SEQUEST-like scoring function. The algorithms were implemented and tested on experimental data. For post-translational modifications, we allow arbitrary number of any modification to a protein. AVAILABILITY: The executable program and other supplementary materials are available online at: http://hto-c.usc.edu:8000/msms/suffix/.     

Undecagold labeling of a glycoprotein: STEM visualization of an undecagoldphosphine cluster labeling the carbohydrate sites of human haptoglobin-hemoglobin complex

A new type of label for electron microscopy has been introduced recently which consists of 11 gold atoms in a compact stable cluster with an organic shell composed of primary amine-substituted phosphine ligands. The radius of the cluster is about 10 A. The (phosphine ligand) amines can be derivatized or allowed to react directly forming covalent bonds to specific sites of other molecules. This report describes the specific labeling of carbohydrate moietis on the glycoprotein human haptoglobin (Hp) in the haptoglobin-hemoglobin complex (Hp X Hb). The Hp X Hb complex is easily recognized in the EM as a barbell-shaped molecule. Only the Hp portion contains carbohydrate (eight carbohydrate chains per Hp X Hb). The carbohydrate moieties of the Hp X Hb complex were oxidized by sodium periodate to produce aldehydes. The primary amines on the undecagold cluster were allowed to react with the aldehyde residues to produce Schiff's base linkages which were subsequently reduced with sodium borohydride. Micrographs obtained on the Brookhaven National Laboratory high-resolution scanning transmission electron microscope (STEM) showed the undecagold label to be localized in a region known to be occupied by the heavy chains of haptoglobin. The amount of labeling was found to be two to four gold clusters per molecule when excess label was reacted. The variation in position of the label is discussed and may be due to flexibility of the carbohydrate chains. Control experiments ruled out nonspecific binding of the gold cluster to the Hp X Hb. The high chemical specificity of the reaction and the high resolution of the gold cluster should make this new label of widespread value in studies of other glycoproteins or carbohydrate-bearing molecules.     

ProViz: protein interaction visualization and exploration

SUMMARY: ProViz is a tool for the visualization of protein-protein interaction networks, developed by the IntAct European project. It provides facilities for navigating in large graphs and exploring biologically relevant features, and adopts emerging standards such as GO and PSI-MI. AVAILABILITY: ProViz is available under the GPL and may be freely downloaded. Source code and binaries are available at http://cbi.labri.fr/eng/proviz.htm CONTACT: david.sherman@labri.fr     

Iron-sulfur cluster biosynthesis in bacteria: Mechanisms of cluster assembly and transfer

Iron-sulfur [Fe-S] clusters are ubiquitous ancient prosthetic groups that are required to sustain fundamental life processes. Formation of intracellular [Fe-S] clusters does not occur spontaneously but requires a complex biosynthetic machinery. Different types of [Fe-S] cluster assembly systems have been discovered. All of them have in common the requirement of a cysteine desulfurase and the participation of [Fe-S] scaffold proteins. The purpose of this review is to discuss various aspects of the molecular mechanisms of [Fe-S] cluster assembly in living organisms: (i) mechanism of sulfur donor enzymes, namely the cysteine desulfurases; (ii) mechanism by which clusters are preassembled on scaffold proteins and (iii) mechanism of [Fe-S] cluster transfer from scaffold to target proteins.