FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression

BACKGROUND: While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. RESULTS: We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. Steps are taken to ensure that the annotation is self-consistent and that the structure of GO is used to identify higher level functions that may not be annotated directly. An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. In a case study, a set of genes, that had statistically significant regression between gene expression levels and environmental temperature along the Atlantic Coast, shows a statistically significant (P < 0.001) enrichment in genes associated with amine metabolism. CONCLUSION: The methods described have application for functional genomics studies, particularly among non-model organisms. The web interface for FunnyBase can be accessed at . Data and source code are available by request at [email protected]

Discovering and linking public omics data sets using the Omics Discovery Index.

Biomedical data are being produced at an unprecedented rate owing to the falling cost of experiments and wider access to genomics, transcriptomics, proteomics and metabolomics platforms1, 2. As a result, public deposition of omics data is on the increase. This presents new challenges, including finding ways to store, organize and access different types of biomedical data stored on different platforms. Here, we present the Omics Discovery Index (OmicsDI; http://www.omicsdi.org), an open-source platform that enables access, discovery and dissemination of omics data sets

Common genetic variation in the <em>HLA</em> region is associated with late-onset sporadic Parkinson's disease

Parkinson’s diseas

NCBI-Hackathons/svcompare: Initial release

This is the first release of this project to annotate and compare SVs

Tools for annotation and comparison of structural variation [version 1; referees: 1 approved, 2 approved with reservations]

The impact of structural variants (SVs) on a variety of organisms and diseases like cancer has become increasingly evident. Methods for SV detection when studying genomic differences across cells, individuals or populations are being actively developed. Currently, just a few methods are available to compare different SVs callsets, and no specialized methods are available to annotate SVs that account for the unique characteristics of these variant types. Here, we introduce SURVIVOR_ant, a tool that compares types and breakpoints for candidate SVs from different callsets and enables fast comparison of SVs to genomic features such as genes and repetitive regions, as well as to previously established SV datasets such as from the 1000 Genomes Project. As proof of concept we compared 16 SV callsets generated by different SV calling methods on a single genome, the Genome in a Bottle sample HG002 (Ashkenazi son), and annotated the SVs with gene annotations, 1000 Genomes Project SV calls, and four different types of repetitive regions. Computation time to annotate 134,528 SVs with 33,954 of annotations was 22 seconds on a laptop

CrossSearch, a User-friendly Search Engine for Detecting Chemically Cross-linked Peptides in Conjugated Proteins*S⃞

Chemical cross-linking and high resolution MS have been integrated successfully to capture protein interactions and provide low resolution structural data for proteins that are refractive to analyses by NMR or crystallography. Despite the versatility of these combined techniques, the array of products that is generated from the cross-linking and proteolytic digestion of proteins is immense and generally requires the use of labeling strategies and/or data base search algorithms to distinguish actual cross-linked peptides from the many side products of cross-linking. Most strategies reported to date have focused on the analysis of small cross-linked protein complexes (<60 kDa) because the number of potential forms of covalently modified peptides increases dramatically with the number of peptides generated from the digestion of such complexes. We report herein the development of a user-friendly search engine, CrossSearch, that provides the foundation for an overarching strategy to detect cross-linked peptides from the digests of large (≥170-kDa) cross-linked proteins, i.e. conjugates. Our strategy combines the use of a low excess of cross-linker, data base searching, and Fourier transform ion cyclotron resonance MS to experimentally minimize and theoretically cull the side products of cross-linking. Using this strategy, the (αβγδ)4 phosphorylase kinase model complex was cross-linked to form with high specificity a 170-kDa βγ conjugate in which we identified residues involved in the intramolecular cross-linking of the 125-kDa β subunit between its regulatory N terminus and its C terminus. This finding provides an explanation for previously published homodimeric two-hybrid interactions of the β subunit and suggests a dynamic structural role for the regulatory N terminus of that subunit. The results offer proof of concept for the CrossSearch strategy for analyzing conjugates and are the first to reveal a tertiary structural element of either homologous α or β regulatory subunit of phosphorylase kinase

STUDY 3: Dark Tobacco Cured Leaf Response to Foliar Calcium Supplements

In collaboration with the University of Kentucky, Murray State University set 12 plots of dark tobacco in an attempt to determine if the leaf quality for cigar wrapper tobacco could be enhanced with the use of foliar calcium. Cigar wrapper leaves serve as a niche market for dark tobacco. Currently, the dark fire tobacco grown in Tennessee and Kentucky provide a secondary vein that is quite large, leading to an unappealing yellowish stripe in the leaf wrapper when the cured leaf is used. Calcium is known to interact with cell wall structure, and is believed to impact color and size of the secondary vein upon curing. Calcium chelate, a dry form calcium supplement, and Helena, a liquid form calcium supplement, were used throughout the treatments. The Narrowleaf Hybrid Madole variety was set on June 10, with 4,900 plants per acre. Spacing consisted of 40 inch rows and 32 inch plant spacing. There were three total treatments used for the experiment. Treatment 1 was an untreated control. Treatment 2 used calcium chelate at a rate of 1 lb/acre, with four different applications throughout the growing process. Treatment 3 used Helena calcium supplement at a rate of 1 quart/acre with the same four applications as treatment 3. A four nozzle boom with 15 gal/acre capacity was used for the applications. Once the tobacco has been cured, the results will demonstrate whether applying either one or both of these calcium sources is beneficial to producers in terms of enhancing uniformity in leaf appearance