Integrated analysis of DNA copy number and gene expression microarray data using gene sets

Background  

Genes that play an important role in tumorigenesis are expected to show association between DNA copy number and RNA expression. Optimal power to find such associations can only be achieved if analysing copy number and gene expression jointly. Furthermore, some copy number changes extend over larger chromosomal regions affecting the expression levels of multiple resident genes.     

Complex coevolutionary history of symbiotic Bacteroidales bacteria of various protists in the gut of termites

Background  

The microbial community in the gut of termites is responsible for the efficient decomposition of recalcitrant lignocellulose. Prominent features of this community are its complexity and the associations of prokaryotes with the cells of cellulolytic flagellated protists. Bacteria in the order Bacteroidales are involved in associations with a wide variety of gut protist species as either intracellular endosymbionts or surface-attached ectosymbionts. In particular, ectosymbionts exhibit distinct morphological patterns of the associations. Therefore, these Bacteroidales symbionts provide an opportunity to investigate not only the coevolutionary relationships with the host protists and their morphological evolution but also how symbiotic associations between prokaryotes and eukaryotes occur and evolve within a complex symbiotic community.     

A migraine variant with abdominal colic and Alice in wonderland syndrome: a case report and review

Background  

Abdominal migraine is a commonly described migraine variant in children and young adults, but associations with Alice in Wonderland syndrome and lilliputian hallucinations are exceptional.     

A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis

Background  

The success achieved by genome-wide association (GWA) studies in the identification of candidate loci for complex diseases has been accompanied by an inability to explain the bulk of heritability. Here, we describe the algorithm V-Bay, a variational Bayes algorithm for multiple locus GWA analysis, which is designed to identify weaker associations that may contribute to this missing heritability.     

Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations

Background  

Most cellular processes are carried out by multi-protein complexes, groups of proteins that bind together to perform a specific task. Some proteins form stable complexes, while other proteins form transient associations and are part of several complexes at different stages of a cellular process. A better understanding of this higher-order organization of proteins into overlapping complexes is an important step towards unveiling functional and evolutionary mechanisms behind biological networks.     

Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study

Introduction  

We aimed to replicate the strong associations that a recent genome wide association study (GWAS) has found between 16 single nucleotide polymorphisms (SNPs) and response to anti-tumour necrosis factor (TNF) treatment in 89 patients with rheumatoid arthritis (RA). This study is very important because, according to published simulations, associations as strong as the reported ones will mean that these SNPs could be used as predictors of response at the individual level.     

Inferring drug-disease associations from integration of chemical,genomic and phenotype data using network propagation

Background

During the last few years, the knowledge of drug, disease phenotype and protein has been rapidly accumulated and more and more scientists have been drawn the attention to inferring drug-disease associations by computational method. Development of an integrated approach for systematic discovering drug-disease associations by those informational data is an important issue.

Methods

We combine three different networks of drug, genomic and disease phenotype and assign the weights to the edges from available experimental data and knowledge. Given a specific disease, we use our network propagation approach to infer the drug-disease associations.

Results

We apply prostate cancer and colorectal cancer as our test data. We use the manually curated drug-disease associations from comparative toxicogenomics database to be our benchmark. The ranked results show that our proposed method obtains higher specificity and sensitivity and clearly outperforms previous methods. Our result also show that our method with off-targets information gets higher performance than that with only primary drug targets in both test data.

Conclusions

We clearly demonstrate the feasibility and benefits of using network-based analyses of chemical, genomic and phenotype data to reveal drug-disease associations. The potential associations inferred by our method provide new perspectives for toxicogenomics and drug reposition evaluation.

     

Jane: a new tool for the cophylogeny reconstruction problem

Background  

This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools.     

Transcriptional analysis of <Emphasis Type="Italic">Pinus sylvestris</Emphasis> roots challenged with the ectomycorrhizal fungus <Emphasis Type="Italic">Laccaria bicolor</Emphasis>

Background  

Symbiotic ectomycorrhizal associations of fungi with forest trees play important and economically significant roles in the nutrition, growth and health of boreal forest trees, as well as in nutrient cycling. The ecology and physiology of ectomycorrhizal associations with Pinus sp are very well documented but very little is known about the molecular mechanisms behind these mutualistic interactions with gymnosperms as compared to angiosperms.     

Restrictive pulmonary function is more prevalent in patients with ankylosing spondylitis than in matched population controls and is associated with impaired spinal mobility: a comparative study

Introduction  

Pulmonary involvement is a known manifestation in patients with ankylosing spondylitis (AS). However, previous studies have been based on small samples and the reported prevalence and associations with typical clinical features vary. The purpose of this study was to compare pulmonary function (PF) in patients with AS and population controls, and to study associations between PF and disease related variables, cardio-respiratory fitness and demographic variables in patients with AS.     

The Ischemic Stroke Genetics Study (ISGS) Protocol

Background  

The molecular basis for the genetic risk of ischemic stroke is likely to be multigenic and influenced by environmental factors. Several small case-control studies have suggested associations between ischemic stroke and polymorphisms of genes that code for coagulation cascade proteins and platelet receptors. Our aim is to investigate potential associations between hemostatic gene polymorphisms and ischemic stroke, with particular emphasis on detailed characterization of the phenotype.     

Associations between the <Emphasis Type="Italic">HLA-A</Emphasis>polymorphism and the clinical manifestations of Behcet's disease

Introduction  

The objective was to investigate associations between the HLA-A gene and Behcet's disease (BD) and its clinical manifestations.     

Rheumatoid cachexia is associated with dyslipidemia and low levels of atheroprotective natural antibodies against phosphorylcholine but not with dietary fat in patients with rheumatoid arthritis: a cross-sectional study

Introduction  

Patients with rheumatoid arthritis (RA) have an increased risk for cardiovascular disease (CVD) independent of traditional risk factors. The aim of this study was to analyze the associations between diet, body composition, lipids and atheroprotective natural antibodies against phosphorylcholine (anti-PC) in patients with RA.     

The association between leptin,interleukin-6, and hip radiographic osteoarthritis in older people: a cross-sectional study

Introduction  

The associations between leptin, interleukin (IL)-6, and hip radiographic osteoarthritis (OA) have not been reported, and their roles in obesity-related hip OA are unclear. The aim of this study was to describe the associations between leptin, IL-6, and hip radiographic osteoarthritis (ROA) in older adults.     

Constipation and diarrhoea - common adverse drug reactions? A cross sectional study in the general population

Background  

Constipation and diarrhoea are common complaints and often reported as adverse drug reactions. This study aimed at finding associations between drugs and constipation and diarrhoea in a general population.     

Testing whether macroevolution follows microevolution: Are colour differences among swans (<Emphasis Type="Italic">Cygnus</Emphasis>) attributable to variation at the <Emphasis Type="Italic">MC1R</Emphasis> locus?

Background  

The MC1R (melanocortin-1 receptor) locus underlies intraspecific variation in melanin-based dark plumage coloration in several unrelated birds with plumage polymorphisms. There is far less evidence for functional variants of MC1R being involved in interspecific variation, in which spurious genotype-phenotype associations arising through population history are a far greater problem than in intraspecific studies. We investigated the relationship between MC1R variation and plumage coloration in swans (Cygnus), which show extreme variation in melanic plumage phenotypes among species (white to black).     

Comparison of phylogenetic trees through alignment of embedded evolutionary distances

Background  

The understanding of evolutionary relationships is a fundamental aspect of modern biology, with the phylogenetic tree being a primary tool for describing these associations. However, comparison of trees for the purpose of assessing similarity and the quantification of various biological processes remains a significant challenge.     

Mating system drives negative associations between morphological features in <Emphasis Type="Italic">Schistosomatidae</Emphasis>

Background  

Sexual morphological features are known to be associated with the mating systems of several animal groups. However, it has been suggested that morphological features other than sexual characteristics could also be constrained by the mating system as a consequence of negative associations. Schistosomatidae are parasitic organisms that vary in mating system and can thus be used to explore links between the mating system and negative associations with morphological features.     

Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions

Background  

The risk of common diseases is likely determined by the complex interplay between environmental and genetic factors, including single nucleotide polymorphisms (SNPs). Traditional methods of data analysis are poorly suited for detecting complex interactions due to sparseness of data in high dimensions, which often occurs when data are available for a large number of SNPs for a relatively small number of samples. Validation of associations observed using multiple methods should be implemented to minimize likelihood of false-positive associations. Moreover, high-throughput genotyping methods allow investigators to genotype thousands of SNPs at one time. Investigating associations for each individual SNP or interactions between SNPs using traditional approaches is inefficient and prone to false positives.