JNets: Exploring networks by integrating annotation

<p>Abstract</p> <p>Background</p> <p>A common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biological systems, particularly when these tools offer analysis capabilities. However, most published network visualizations are static representations that do not support user interaction.</p> <p>Results</p> <p>JNets was designed as a network visualization tool that incorporates annotation to explore the underlying features of interaction networks. The software is available as an application and a configurable applet that can provide a flexible and dynamic online interface to many types of network data. As a case study, we use JNets to investigate approved drug targets present within the HIV-1 Human protein interaction network. Our software highlights the intricate influence that HIV-1 has on the host immune response.</p> <p>Conclusion</p> <p>JNets is a software tool that allows interaction networks to be visualized and studied remotely, from within a standard web page. Therefore, using this free software, network data can be presented in an enhanced, interactive format. More information about JNets is available at <url>http://www.manchester.ac.uk/bioinformatics/jnets</url>.</p

JNets: Exploring networks by integrating annotation

<p>Abstract</p> <p>Background</p> <p>A common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biological systems, particularly when these tools offer analysis capabilities. However, most published network visualizations are static representations that do not support user interaction.</p> <p>Results</p> <p>JNets was designed as a network visualization tool that incorporates annotation to explore the underlying features of interaction networks. The software is available as an application and a configurable applet that can provide a flexible and dynamic online interface to many types of network data. As a case study, we use JNets to investigate approved drug targets present within the HIV-1 Human protein interaction network. Our software highlights the intricate influence that HIV-1 has on the host immune response.</p> <p>Conclusion</p> <p>JNets is a software tool that allows interaction networks to be visualized and studied remotely, from within a standard web page. Therefore, using this free software, network data can be presented in an enhanced, interactive format. More information about JNets is available at <url>http://www.manchester.ac.uk/bioinformatics/jnets</url>.</p

MicroRNAs from the same precursor have different targeting properties

UnlabelledBackgroundThe processing of a microRNA results in an intermediate duplex of two potential mature products that derive from the two arms (5' and 3') of the precursor hairpin. It is often suggested that one of the sequences is degraded and the other is incorporated into the RNA-induced silencing complex. However, both precursor arms may give rise to functional levels of mature microRNA and the dominant product may change from species to species, from tissue to tissue, or between developmental stages. Therefore, both arms of the precursor have the potential to produce functional mature microRNAs.ResultsWe have investigated the relationship between predicted mRNA targets of mature sequences derived from the 5' and 3' arms of the same pre-microRNAs. Using six state-of-the-art target prediction algorithms, we find that 5'/3' microRNA pairs target different sites in 3' untranslated regions of mRNAs. We also find that these pairs do not generally target overlapping sets of genes, or functionally related genes.ConclusionsWe show that alternative mature products produced from the same precursor microRNAs have different targeting properties and therefore different biological functions. These data strongly suggest that developmental or evolutionary changes in arm choice will have significant functional consequences

Child oral health and preventive dental service access among children with intellectual disabilities, autism and other educational additional support needs: a population-based record linkage cohort study

Objective: Inequalities in child oral health are a global challenge and the intersection of socioeconomic factors with educational additional support needs (ASN), including children with intellectual disabilities or autism, have thus far received limited attention in relatively small clinical studies. We aimed to address this evidence gap by investigating oral health and access to preventive dental services among children with ASN compared to the general child population. Methods: Cohort study linking data from six Scotland-wide health and education databases compared: dental caries experience and tooth extraction via general anaesthetic; receipt of school-based dental inspection; access to primary care and hospital dental services; and access to the Childsmile national oral health improvement programme between children with a range of ASN (intellectual disabilities, autism, social and other) and their peers for the school years 2016/17–2018/19 (n = 166 781). Results: Children with any ASN had higher rates of caries experience than those with no ASN, however, after adjustment for socioeconomic deprivation, sex, year, and school type only those with a social or other ASN remained at increased risk. Rates of tooth extraction under general anaesthesia in hospital were higher among children with intellectual disabilities (aRR = 1.67;95% CI = [1.16–2.37]). School-based dental inspection access improved for children with intellectual disability and/or autism from 2016/17 onwards, although higher rates of child refusal on the day were observed in these groups (no ASN refusal: 5.4%; intellectual disability: 35.8%; autism: 40.3%). Children with any ASN were less likely to attend primary dental-care regularly, and in those who attended, children with intellectual disability or autism were less likely than their peers to receive prevention (fluoride varnish, oral-hygiene instruction, or dietary advice). Childsmile nursery-supervised toothbrushing programme access among children with any ASN was similar to children with no ASN and children with intellectual disability (aRR = 1.27;95% CI = [1.12–1.45]) or autism (aRR = 1.32;95% CI = [1.19–1.45]) were more likely to receive support from Childsmile dental health support worker. Conclusions: We have identified inequalities in oral health and dental care for children with different ASN in Scotland with both a greater burden of disease among some groups and higher complexity of care; compounded by reduced and variable access to preventive dental services. Further efforts are needed to develop and improve preventive care pathways for children with ASN and integrate oral health to wider healthcare systems for these children to mitigate against oral health inequalities

Evaluation of a national complex oral health improvement programme: a population data linkage cohort study in Scotland

Objectives Child dental caries is a global public health challenge with high prevalence and wide inequalities. A complex public health programme (Childsmile) was established. We aimed to evaluate the reach of the programme and its impact on child oral health. Setting Education, health and community settings, Scotland-wide. Interventions Childsmile (national oral health improvement programme) interventions: nursery-based fluoride varnish applications (FVAs) and supervised daily toothbrushing, community-based Dental Health Support Worker (DHSW) contacts and primary care dental practice visits—delivered to the population via a proportionate universal approach. Participants: 50 379 children (mean age=5.5 years, SD=0.3) attending local authority schools (2014/2015). Design: Population-based individual child-level data on four Childsmile interventions linked to dental inspection survey data to form a longitudinal cohort. Logistic regression assessed intervention reach and the independent impact of each intervention on caries experience, adjusting for age, sex and area-based Scottish Index of Multiple Deprivation (SIMD). Outcome measures: Reach of the programme is defined as the percentage of children receiving each intervention at least once by SIMD fifth. Obvious dental caries experience (presence/absence) is defined as the presence of decay (into dentine), missing (extracted) due to decay or filled deciduous teeth. Results: 15 032 (29.8%) children had caries experience. The universal interventions had high population reach: nursery toothbrushing (89.1%), dental practice visits (70.5%). The targeted interventions strongly favoured children from the most deprived areas: DHSW contacts (SIMD 1: 29.5% vs SIMD 5: 7.7%), nursery FVAs (SIMD 1: 75.2% vs SIMD 5: 23.2%). Odds of caries experience were markedly lower among children participating in nursery toothbrushing (&gt;3 years, adjusted OR (aOR)=0.60; 95% CI 0.55 to 0.66) and attending dental practice (≥6 visits, aOR=0.55; 95% CI 0.50 to 0.61). The findings were less clear for DHSW contacts. Nursery FVAs were not independently associated with caries experience. Conclusions: The universal interventions, nursery toothbrushing and regular dental practice visits were independently and most strongly associated with reduced odds of caries experience in the cohort, with nursery toothbrushing having the greatest impact among children in areas of high deprivation

Patterns of HIV-1 Protein Interaction Identify Perturbed Host-Cellular Subsystems

Human immunodeficiency virus type 1 (HIV-1) exploits a diverse array of host cell functions in order to replicate. This is mediated through a network of virus-host interactions. A variety of recent studies have catalogued this information. In particular the HIV-1, Human Protein Interaction Database (HHPID) has provided a unique depth of protein interaction detail. However, as a map of HIV-1 infection, the HHPID is problematic, as it contains curation error and redundancy; in addition, it is based on a heterogeneous set of experimental methods. Based on identifying shared patterns of HIV-host interaction, we have developed a novel methodology to delimit the core set of host-cellular functions and their associated perturbation from the HHPID. Initially, using biclustering, we identify 279 significant sets of host proteins that undergo the same types of interaction. The functional cohesiveness of these protein sets was validated using a human protein-protein interaction network, gene ontology annotation and sequence similarity. Next, using a distance measure, we group host protein sets and identify 37 distinct higher-level subsystems. We further demonstrate the biological significance of these subsystems by cross-referencing with global siRNA screens that have been used to detect host factors necessary for HIV-1 replication, and investigate the seemingly small intersect between these data sets. Our results highlight significant host-cell subsystems that are perturbed during the course of HIV-1 infection. Moreover, we characterise the patterns of interaction that contribute to these perturbations. Thus, our work disentangles the complex set of HIV-1-host protein interactions in the HHPID, reconciles these with siRNA screens and provides an accessible and interpretable map of infection

An Integrated Transcriptomic and Meta-Analysis of Hepatoma Cells Reveals Factors That Influence Susceptibility to HCV Infection

Hepatitis C virus (HCV) is a global problem. To better understand HCV infection researchers employ in vitro HCV cell-culture (HCVcc) systems that use Huh-7 derived hepatoma cells that are particularly permissive to HCV infection. A variety of hyper-permissive cells have been subcloned for this purpose. In addition, subclones of Huh-7 which have evolved resistance to HCV are available. However, the mechanisms of susceptibility or resistance to infection among these cells have not been fully determined. In order to elucidate mechanisms by which hepatoma cells are susceptible or resistant to HCV infection we performed genome-wide expression analyses of six Huh-7 derived cell cultures that have different levels of permissiveness to infection. A great number of genes, representing a wide spectrum of functions are differentially expressed between cells. To focus our investigation, we identify host proteins from HCV replicase complexes, perform gene expression analysis of three HCV infected cells and conduct a detailed analysis of differentially expressed host factors by integrating a variety of data sources. Our results demonstrate that changes relating to susceptibility to HCV infection in hepatoma cells are linked to the innate immune response, secreted signal peptides and host factors that have a role in virus entry and replication. This work identifies both known and novel host factors that may influence HCV infection. Our findings build upon current knowledge of the complex interplay between HCV and the host cell, which could aid development of new antiviral strategies

GO term enrichment among congruent subgraphs.

<p>GO term enrichment among congruent subgraphs.</p

Network of best hits between subgraphs of PPI, genetic and coregulation networks.

<p>Nodes represent individual subgraphs with blue, red or yellow nodes corresponding to subgraphs from the PPI, genetic or co-regulation networks, respectively. Edges represent links between subgraphs with a statistically significant intersection of genes with an MCC . Only the best intersection between each network comparison, defined by MCC score, is shown. Letters A to D indicate high-degree neighbourhoods that consist of a node with degree and all neighbours of that node.</p