Abstract:
BACKGROUND:Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune suppression if animals are infected with an ncp biotype during early gestation, followed by a subsequent infection of the cp biotype. The molecular mechanisms that underscore the complex disease etiology leading to immune suppression in cattle caused by BVDV are not well understood. RESULTS:Using proteomics, we evaluated the effect of cp and ncp BVDV infection of bovine monocytes to determine their role in viral immune suppression and uncontrolled inflammation. Proteins were isolated by differential detergent fractionation and identified by 2D-LC ESI MS/MS. We identified 137 and 228 significantly altered bovine proteins due to ncp and cp BVDV infection, respectively. Functional analysis of these proteins using the Gene Ontology (GO) showed multiple under- and over- represented GO functions in molecular function, biological process and cellular component between the two BVDV biotypes. Analysis of the top immunological pathways affected by BVDV infection revealed that pathways representing macropinocytosis signalling, virus entry via endocytic pathway, integrin signalling and primary immunodeficiency signalling were identified only in ncp BVDV-infected monocytes. In contrast, pathways like actin cytoskeleton signalling, RhoA signalling, clathrin-mediated endocytosis signalling and interferon signalling were identified only in cp BDVD-infected cells. Of the six common pathways involved in cp and ncp BVDV infection, acute phase response signalling was the most significant for both BVDV biotypes. Although, most shared altered host proteins between both BVDV biotypes showed the same type of change, integrin alpha 2b (ITGA2B) and integrin beta 3 (ITGB3) were down- regulated by ncp BVDV and up- regulated by cp BVDV infection. CONCLUSIONS:This study shows that, as we expected, there are significant functional differences in the host proteins that respond to cp or ncp BVDV infection. The combined use of GO and systems biology network modelling facilitated a better understanding of host-pathogen interactions.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Ammari M,McCarthy FM,Nanduri B,Pinchuk LMdoi
10.1186/1471-2105-11-S6-S9subject
Has Abstractpub_date
2010-10-07 00:00:00pages
S9issn
1471-2105pii
1471-2105-11-S6-S9journal_volume
11 Suppl 6pub_type
杂志文章abstract:BACKGROUND:The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in identifying putative biomarkers of disease from high-dimensional proteomic mass spectral data. In pa...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S9-S16
更新日期:2009-09-17 00:00:00
abstract:BACKGROUND:Although high-throughput microarray based molecular diagnostic technologies show a great promise in cancer diagnosis, it is still far from a clinical application due to its low and instable sensitivities and specificities in cancer molecular pattern recognition. In fact, high-dimensional and heterogeneous tu...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S1-S7
更新日期:2011-02-15 00:00:00
abstract:BACKGROUND:A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal gen...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2469-7
更新日期:2018-12-28 00:00:00
abstract:BACKGROUND:Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-111
更新日期:2004-08-14 00:00:00
abstract:BACKGROUND:Transcription factor binding sites (TFBSs) are crucial in the regulation of gene transcription. Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used to identify potential regulatory sequences, but the procedure can only map the probable protein-DNA...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S12-S7
更新日期:2008-12-12 00:00:00
abstract:BACKGROUND:Scientific workflows management systems are increasingly used to specify and manage bioinformatics experiments. Their programming model appeals to bioinformaticians, who can use them to easily specify complex data processing pipelines. Such a model is underpinned by a graph structure, where nodes represent b...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S1-S12
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:An important question in the analysis of biochemical data is that of identifying subsets of molecular variables that may jointly influence a biological response. Statistical variable selection methods have been widely used for this purpose. In many settings, it may be important to incorporate ancillary biolo...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-94
更新日期:2012-05-11 00:00:00
abstract:BACKGROUND:Mixed models have a long and fruitful history in statistics. They are pertinent to genomics problems because they are highly versatile, accommodating a wide variety of situations within the same theoretical and algorithmic framework. RESULTS:Qxpak is a package for versatile statistical genomics, specificall...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-202
更新日期:2011-05-25 00:00:00
abstract:BACKGROUND:Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs oft...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-102
更新日期:2007-03-26 00:00:00
abstract:BACKGROUND:Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain datab...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-4-16
更新日期:2003-05-06 00:00:00
abstract:BACKGROUND:For successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significant...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-471
更新日期:2007-12-03 00:00:00
abstract:BACKGROUND:Gene expression microarray experiments are expensive to conduct and guidelines for acceptable quality control at intermediate steps before and after the samples are hybridised to chips are vague. We conducted an experiment hybridising RNA from human brain to 117 U133A Affymetrix GeneChips and used these data...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-211
更新日期:2006-04-19 00:00:00
abstract:BACKGROUND:In the past decade, bioinformatics tools have matured enough to reliably perform sophisticated primary data analysis on Next Generation Sequencing (NGS) data, such as mapping, assemblies and variant calling, however, there is still a dire need for improvements in the higher level analysis such as NGS data or...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-167
更新日期:2013-05-28 00:00:00
abstract:BACKGROUND:In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell surface shedding is an exemplary application area of this approach. RESULTS:We developed ImproViser...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-207
更新日期:2014-06-19 00:00:00
abstract:BACKGROUND:Antibacterial peptides are important components of the innate immune system, used by the host to protect itself from different types of pathogenic bacteria. Over the last few decades, the search for new drugs and drug targets has prompted an interest in these antibacterial peptides. We analyzed 486 antibacte...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-263
更新日期:2007-07-23 00:00:00
abstract:BACKGROUND:Protein structure prediction has achieved a lot of progress during the last few decades and a greater number of models for a certain sequence can be predicted. Consequently, assessing the qualities of predicted protein models in perspective is one of the key components of successful protein structure predict...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1691-z
更新日期:2017-05-25 00:00:00
abstract:BACKGROUND:PCR clonal artefacts originating from NGS library preparation can affect both genomic as well as RNA-Seq applications when protocols are pushed to their limits. In RNA-Seq however the artifactual reads are not easy to tell apart from normal read duplication due to natural over-sequencing of highly expressed ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1276-2
更新日期:2016-10-21 00:00:00
abstract::Transcript quantification is a long-standing problem in genomics and estimating the relative abundance of alternatively-spliced isoforms from the same transcript is an important special case. Both problems have recently been illuminated by high-throughput RNA sequencing experiments which are quickly generating large a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S6-S11
更新日期:2012-04-19 00:00:00
abstract:BACKGROUND:The advent of RNA interference techniques enables the selective silencing of biologically interesting genes in an efficient way. In combination with DNA microarray technology this enables researchers to gain insights into signaling pathways by observing downstream effects of individual knock-downs on gene ex...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-386
更新日期:2007-10-15 00:00:00
abstract:BACKGROUND:The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-d...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-322
更新日期:2013-11-14 00:00:00
abstract:BACKGROUND:The analysis of mass spectra suggests that the existence of derivative peaks is strongly dependent on the intensity of the primary peaks. Peak selection from tandem mass spectrum is used to filter out noise and contaminant peaks. It is widely accepted that a valid primary peak tends to have high intensity an...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-346
更新日期:2011-08-17 00:00:00
abstract:BACKGROUND:Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-282
更新日期:2011-07-12 00:00:00
abstract:BACKGROUND:Activities of drug molecules can be predicted by QSAR (quantitative structure activity relationship) models, which overcomes the disadvantages of high cost and long cycle by employing the traditional experimental method. With the fact that the number of drug molecules with positive activity is rather fewer t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S6-S7
更新日期:2008-05-28 00:00:00
abstract:BACKGROUND:Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis methods if meaningful biological conclusions are to be drawn. For example, a range of traditional s...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0358-2
更新日期:2014-11-04 00:00:00
abstract:BACKGROUND:Human triosephosphate isomerase (HsTIM) deficiency is a genetic disease caused often by the pathogenic mutation E104D. This mutation, located at the side of an abnormally large cluster of water in the inter-subunit interface, reduces the thermostability of the enzyme. Why and how these water molecules are di...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-S16-S11
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:In many biomedical applications, there is a need for developing classification models based on noisy annotations. Recently, various methods addressed this scenario by relaying on unreliable annotations obtained from multiple sources. RESULTS:We proposed a probabilistic classification algorithm based on labe...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-S12-S5
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. RESULTS:We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifica...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2160-z
更新日期:2018-04-25 00:00:00
abstract::Advances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher sys...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S17-I1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes....
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S1-S55
更新日期:2010-01-18 00:00:00
abstract:BACKGROUND:The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caeno...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-250
更新日期:2006-05-08 00:00:00