Abstract:
BACKGROUND:Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expressed in microarray experiments is challenging because of their potentially high type I error rate. Methods for large-scale statistical analyses have been developed but most of them are applicable to two-sample or two-condition data. RESULTS:We developed a large-scale multiple-group F-test based method, named ranking analysis of F-statistics (RAF), which is an extension of ranking analysis of microarray data (RAM) for two-sample t-test. In this method, we proposed a novel random splitting approach to generate the null distribution instead of using permutation, which may not be appropriate for microarray data. We also implemented a two-simulation strategy to estimate the false discovery rate. Simulation results suggested that it has higher efficiency in finding differentially expressed genes among multiple classes at a lower false discovery rate than some commonly used methods. By applying our method to the experimental data, we found 107 genes having significantly differential expressions among 4 treatments at <0.7% FDR, of which 31 belong to the expressed sequence tags (ESTs), 76 are unique genes who have known functions in the brain or central nervous system and belong to six major functional groups. CONCLUSION:Our method is suitable to identify differentially expressed genes among multiple groups, in particular, when sample size is small.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Tan YD,Fornage M,Xu Hdoi
10.1186/1471-2105-9-142subject
Has Abstractpub_date
2008-03-06 00:00:00pages
142issn
1471-2105pii
1471-2105-9-142journal_volume
9pub_type
杂志文章abstract:BACKGROUND:Failure on Highly Active Anti-Retroviral Treatment is often accompanied with development of antiviral resistance to one or more drugs included in the treatment. In general, the virus is more likely to develop resistance to drugs with a lower genetic barrier. Previously, we developed a method to reverse engin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-409
更新日期:2010-08-03 00:00:00
abstract:BACKGROUND:One of the main goals in cancer studies including high-throughput microRNA (miRNA) and mRNA data is to find and assess prognostic signatures capable of predicting clinical outcome. Both mRNA and miRNA expression changes in cancer diseases are described to reflect clinical characteristics like staging and pro...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-488
更新日期:2011-12-21 00:00:00
abstract:BACKGROUND:The Triplex cell vaccine is a cancer cellular vaccine that can prevent almost completely the mammary tumor onset in HER-2/neu transgenic mice. In a translational perspective, the activity of the Triplex vaccine was also investigated against lung metastases showing that the vaccine is an effective treatment a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S7-S13
更新日期:2010-10-15 00:00:00
abstract:BACKGROUND:Protein-protein interactions (PPIs) are central to many biological processes. Considering that the experimental methods for identifying PPIs are time-consuming and expensive, it is important to develop automated computational methods to better predict PPIs. Various machine learning methods have been proposed...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03646-8
更新日期:2020-07-21 00:00:00
abstract:BACKGROUND:Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. DESCRIPTION:Here we present...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-70
更新日期:2006-02-15 00:00:00
abstract:BACKGROUND:The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-cou...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-254
更新日期:2006-05-15 00:00:00
abstract:BACKGROUND:Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings i...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-421
更新日期:2009-12-15 00:00:00
abstract:BACKGROUND:Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is essential for epidemiology, diagnostics, and vaccine development. Strain recognition based on similar...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-379
更新日期:2007-10-10 00:00:00
abstract:BACKGROUND:The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relations...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0866-8
更新日期:2016-01-05 00:00:00
abstract:BACKGROUND:Reference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication. The higher the quality of a reference genome assembly the more accurate the downstream analysis will be. During the last few years, major efforts have been made towards improving the qua...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1735-4
更新日期:2017-06-30 00:00:00
abstract:BACKGROUND:Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to populatio...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-255
更新日期:2013-08-21 00:00:00
abstract:BACKGROUND:The rabbit is an important model organism used in a wide range of biomedical research. However, the rabbit genome is still sparsely annotated, thus prohibiting extensive functional analysis of gene sets derived from whole-genome experiments. We developed a web-based application that provides augmented annota...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-84
更新日期:2012-05-08 00:00:00
abstract:BACKGROUND:Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role in protein-protein docking. Despite significant progresses, shape representation remains an open que...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3270-y
更新日期:2019-12-24 00:00:00
abstract:BACKGROUND:The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologist...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-264
更新日期:2008-06-05 00:00:00
abstract:BACKGROUND:A large number of experimental studies show that the mutation and regulation of long non-coding RNAs (lncRNAs) are associated with various human diseases. Accurate prediction of lncRNA-disease associations can provide a new perspective for the diagnosis and treatment of diseases. The main function of many ln...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03721-0
更新日期:2020-09-03 00:00:00
abstract:BACKGROUND:Severity gradation of missense mutations is a big challenge for exome annotation. Predictors of deleteriousness that are most frequently used to filter variants found by next generation sequencing, produce qualitative predictions, but also numerical scores. It has never been tested if these scores correlate ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2416-7
更新日期:2018-11-30 00:00:00
abstract:BACKGROUND:Testing the dependence of two variables is one of the fundamental tasks in statistics. In this work, we developed an open-source R package (knnAUC) for detecting nonlinear dependence between one continuous variable X and one binary dependent variables Y (0 or 1). RESULTS:We addressed this problem by using k...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2427-4
更新日期:2018-11-22 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:Activation of naïve B lymphocytes by extracellular ligands, e.g. antigen, lipopolysaccharide (LPS) and CD40 ligand, induces a combination of common and ligand-specific phenotypic changes through complex signal transduction pathways. For example, although all three of these ligands induce proliferation, only ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-237
更新日期:2006-05-02 00:00:00
abstract:BACKGROUND:Inflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a long series of pathologic events that started years before. The systemic characteristics and relate...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2413-x
更新日期:2018-11-30 00:00:00
abstract:BACKGROUND:In metabolomics experiments, spectral fingerprints of metabolites with no known structural identity are detected routinely. Computer-assisted structure elucidation (CASE) has been used to determine the structural identities of unknown compounds. It is generally accepted that a single 1D NMR spectrum or mass ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-234
更新日期:2014-07-05 00:00:00
abstract::Time course gene expression experiments are a popular means to infer co-expression. Many methods have been proposed to cluster genes or to build networks based on similarity measures of their expression dynamics. In this paper we apply a correlation based approach to network reconstruction to three datasets of time se...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S1-S16
更新日期:2007-03-08 00:00:00
abstract:BACKGROUND:High-throughput sequencing has rapidly become an essential part of precision cancer medicine. But validating results obtained from analyzing and interpreting genomic data remains a rate-limiting factor. The gold standard, of course, remains manual validation by expert panels, which is not without its weaknes...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2440-7
更新日期:2018-11-19 00:00:00
abstract:BACKGROUND:Sequence comparison is one of the most prominent tools in biological research, and is instrumental in studying gene function and evolution. The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in prote...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-199
更新日期:2006-04-10 00:00:00
abstract:BACKGROUND:The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cryo-EM data analysis. Template-based particle picking by an objective function using fast local corre...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2714-8
更新日期:2019-04-03 00:00:00
abstract::DNA methylation exhibits different patterns in different cancers. DNA methylation rates at different genomic loci appear to be highly correlated in some samples but not in others. We call such phenomena conditional concordant relationships (CCRs). In this study, we explored DNA methylation patterns in 12 common cancer...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S13-S7
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree constructi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-338
更新日期:2014-10-04 00:00:00
abstract:BACKGROUND:Cyclic nucleotides are ubiquitous intracellular messengers. Until recently, the roles of cyclic nucleotides in plant cells have proven difficult to uncover. With an understanding of the protein domains which can bind cyclic nucleotides (CNB and GAF domains) we scanned the completed genomes of the higher plan...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-6
更新日期:2005-01-11 00:00:00
abstract:BACKGROUND:We introduce Approximate Entropy as a mathematical method of analysis for microarray data. Approximate entropy is applied here as a method to classify the complex gene expression patterns resultant of a clinical sample set. Since Entropy is a measure of disorder in a system, we believe that by choosing genes...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-66
更新日期:2009-02-20 00:00:00
abstract:BACKGROUND:In the biomedical domain, the desired information of a question (query) asked by biologists usually is a list of a certain type of entities covering different aspects that are related to the question, such as genes, proteins, diseases, mutations, etc. Hence it is important for a biomedical information retrie...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S5-S8
更新日期:2011-01-01 00:00:00