Abstract:
BACKGROUND:Differential co-expression (DCX) signifies change in degree of co-expression of a set of genes among different biological conditions. It has been used to identify differential co-expression networks or interactomes. Many algorithms have been developed for single-factor differential co-expression analysis and applied in a variety of studies. However, in many studies, the samples are characterized by multiple factors such as genetic markers, clinical variables and treatments. No algorithm or methodology is available for multi-factor analysis of differential co-expression. RESULTS:We developed a novel formulation and a computationally efficient greedy search algorithm called MultiDCoX to perform multi-factor differential co-expression analysis. Simulated data analysis demonstrates that the algorithm can effectively elicit differentially co-expressed (DCX) gene sets and quantify the influence of each factor on co-expression. MultiDCoX analysis of a breast cancer dataset identified interesting biologically meaningful differentially co-expressed (DCX) gene sets along with genetic and clinical factors that influenced the respective differential co-expression. CONCLUSIONS:MultiDCoX is a space and time efficient procedure to identify differentially co-expressed gene sets and successfully identify influence of individual factors on differential co-expression.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Liany H,Rajapakse JC,Karuturi RKMdoi
10.1186/s12859-017-1963-7subject
Has Abstractpub_date
2017-12-28 00:00:00pages
576issue
Suppl 16issn
1471-2105pii
10.1186/s12859-017-1963-7journal_volume
18pub_type
杂志文章abstract:BACKGROUND:Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discrimin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-56
更新日期:2005-03-15 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:Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipeli...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1592-1
更新日期:2017-03-20 00:00:00
abstract:BACKGROUND:The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-582
更新日期:2010-11-29 00:00:00
abstract:BACKGROUND:Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regions. RESULTS:Here, we weighted edges of a human protein interaction network and a transcriptional r...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-392
更新日期:2010-07-22 00:00:00
abstract:BACKGROUND:Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, can be used to predict potential conformational switches; nevertheless, no existent tool can detec...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S5-S6
更新日期:2012-04-12 00:00:00
abstract:BACKGROUND:Under conditions of no strand bias the number of Gs is equal to that of Cs for each DNA strand; similarly, the total number of Ts is equal to that of As. However, within each strand there are considerable local deviations from the A = T and G = C equality. These asymmetries in nucleotide composition have bee...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-21
更新日期:2007-01-23 00:00:00
abstract:BACKGROUND:Expression profiles obtained from multiple perturbation experiments are increasingly used to reconstruct transcriptional regulatory networks, from well studied, simple organisms up to higher eukaryotes. Admittedly, a key ingredient in developing a reconstruction method is its ability to integrate heterogeneo...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-228
更新日期:2008-05-06 00:00:00
abstract:BACKGROUND:Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactom...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1585-0
更新日期:2017-03-16 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are single-stranded non-coding RNAs known to regulate a wide range of cellular processes by silencing the gene expression at the protein and/or mRNA levels. Computational prediction of miRNA targets is essential for elucidating the detailed functions of miRNA. However, the prediction speci...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-476
更新日期:2010-09-22 00:00:00
abstract:BACKGROUND:Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stringent score cutoff is applied to distinguish putative homologs from possible false positive hits. As a consequence, some BLAST hits are discar...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-86
更新日期:2010-02-12 00:00:00
abstract:BACKGROUND:A massive amount of proteomic data is generated on a daily basis, nonetheless annotating all sequences is costly and often unfeasible. As a countermeasure, machine learning methods have been used to automatically annotate new protein functions. More specifically, many studies have investigated hierarchical m...
journal_title:BMC bioinformatics
pub_type: 杂志文章,评审
doi:10.1186/s12859-019-3060-6
更新日期:2019-09-23 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:MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes ba...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-261
更新日期:2008-06-04 00:00:00
abstract:BACKGROUND:High-throughput methods can directly detect the set of interacting proteins in model species but the results are often incomplete and exhibit high false positive and false negative rates. A number of researchers have recently presented methods for integrating direct and indirect data for predicting interacti...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S10-S6
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-395
更新日期:2010-07-23 00:00:00
abstract:BACKGROUND:A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinform...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S6-S15
更新日期:2009-06-16 00:00:00
abstract:BACKGROUND:Histopathology image analysis is a gold standard for cancer recognition and diagnosis. Automatic analysis of histopathology images can help pathologists diagnose tumor and cancer subtypes, alleviating the workload of pathologists. There are two basic types of tasks in digital histopathology image analysis: i...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1685-x
更新日期:2017-05-26 00:00:00
abstract:BACKGROUND:Intrinsically Disordered Proteins (IDPs) lack an ordered three-dimensional structure and are enriched in various biological processes. The Molecular Recognition Features (MoRFs) are functional regions within IDPs that undergo a disorder-to-order transition on binding to a partner protein. Identifying MoRFs i...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1375-0
更新日期:2016-12-22 00:00:00
abstract:BACKGROUND:Probing the complex fusion of genetic and environmental interactions, metabolic profiling (or metabolomics/metabonomics), the study of small molecules involved in metabolic reactions, is a rapidly expanding 'omics' field. A major technique for capturing metabolite data is 1H-NMR spectroscopy and this yields ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-496
更新日期:2010-10-06 00:00:00
abstract:BACKGROUND:RNA sequencing has become an increasingly affordable way to profile gene expression patterns. Here we introduce a workflow implementing several open-source softwares that can be run on a high performance computing environment. RESULTS:Developed as a tool by the Bioinformatics Shared Resource Group (BISR) at...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3251-1
更新日期:2019-12-20 00:00:00
abstract:BACKGROUND:Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entiti...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1493-3
更新日期:2017-02-02 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:The spatial configuration of chromosomes is essential to various cellular processes, notably gene regulation, while architecture related alterations, such as translocations and gene fusions, are often cancer drivers. Thus, eliciting chromatin conformation is important, yet challenging due to compaction, dyna...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-3424-y
更新日期:2020-02-24 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:In this short article, we discuss a simple method for assessing sample size requirements in microarray experiments. RESULTS:Our method starts with the output from a permutation-based analysis for a set of pilot data, e.g. from the SAM package. Then for a given hypothesized mean difference and various sample...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-106
更新日期:2006-03-02 00:00:00
abstract:BACKGROUND:The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating systems were evaluated from a perspective of annotation. To further explore t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S10-S3
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant data. Shared data science infrastructures like Boag is needed to efficiently process and parse data co...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2967-2
更新日期:2019-08-22 00:00:00
abstract:BACKGROUND:Gene expression measurements from breast cancer (BrCa) tumors are established clinical predictive tools to identify tumor subtypes, identify patients showing poor/good prognosis, and identify patients likely to have disease recurrence. However, diverse breast cancer datasets in conjunction with diagnostic cl...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-63
更新日期:2008-01-28 00:00:00
abstract:BACKGROUND:Word sense disambiguation (WSD) attempts to solve lexical ambiguities by identifying the correct meaning of a word based on its context. WSD has been demonstrated to be an important step in knowledge-based approaches to automatic summarization. However, the correlation between the accuracy of the WSD methods...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-355
更新日期:2011-08-26 00:00:00