Abstract:
BACKGROUND:Multiple co-inertia analysis (mCIA) is a multivariate analysis method that can assess relationships and trends in multiple datasets. Recently it has been used for integrative analysis of multiple high-dimensional -omics datasets. However, its estimated loading vectors are non-sparse, which presents challenges for identifying important features and interpreting analysis results. We propose two new mCIA methods: 1) a sparse mCIA method that produces sparse loading estimates and 2) a structured sparse mCIA method that further enables incorporation of structural information among variables such as those from functional genomics. RESULTS:Our extensive simulation studies demonstrate the superior performance of the sparse mCIA and structured sparse mCIA methods compared to the existing mCIA in terms of feature selection and estimation accuracy. Application to the integrative analysis of transcriptomics data and proteomics data from a cancer study identified biomarkers that are suggested in the literature related with cancer disease. CONCLUSION:Proposed sparse mCIA achieves simultaneous model estimation and feature selection and yields analysis results that are more interpretable than the existing mCIA. Furthermore, proposed structured sparse mCIA can effectively incorporate prior network information among genes, resulting in improved feature selection and enhanced interpretability.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Min EJ,Long Qdoi
10.1186/s12859-020-3455-4subject
Has Abstractpub_date
2020-04-15 00:00:00pages
141issue
1issn
1471-2105pii
10.1186/s12859-020-3455-4journal_volume
21pub_type
杂志文章abstract:BACKGROUND:Microarray technologies produced large amount of data. The hierarchical clustering is commonly used to identify clusters of co-expressed genes. However, microarray datasets often contain missing values (MVs) representing a major drawback for the use of the clustering methods. Usually the MVs are not treated,...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-114
更新日期:2004-08-23 00:00:00
abstract:BACKGROUND:Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff bet...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1518-y
更新日期:2017-02-23 00:00:00
abstract:BACKGROUND:Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0681-2
更新日期:2015-08-19 00:00:00
abstract:BACKGROUND:Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector intensity readings, each uniquely addressed along dimensions of time (e.g., retention time of chemic...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S9-S15
更新日期:2008-08-12 00:00:00
abstract:BACKGROUND:Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2791-8
更新日期:2019-04-27 00:00:00
abstract:BACKGROUND:We develop a probabilistic model for combining kernel matrices to predict the function of proteins. It extends previous approaches in that it can handle multiple labels which naturally appear in the context of protein function. RESULTS:Explicit modeling of multilabels significantly improves the capability o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S2-S12
更新日期:2007-05-03 00:00:00
abstract:BACKGROUND:Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mec...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-414
更新日期:2011-10-25 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:Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-117
更新日期:2007-04-04 00:00:00
abstract:BACKGROUND:Hepatocellular carcinoma (HCC) is an aggressive epithelial tumor which shows very poor prognosis and high rate of recurrence, representing an urgent problem for public healthcare. MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNAs that attract great attention because of their role in regulation of...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0836-1
更新日期:2015-12-10 00:00:00
abstract:BACKGROUND:The increasing availability of Electronic Health Record (EHR) data and specifically free-text patient notes presents opportunities for phenotype extraction. Text-mining methods in particular can help disease modeling by mapping named-entities mentions to terminologies and clustering semantically related term...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-10
更新日期:2013-01-16 00:00:00
abstract:BACKGROUND:It is possible to predict whether a tuberculosis (TB) patient will fail to respond to specific antibiotics by sequencing the genome of the infecting Mycobacterium tuberculosis (Mtb) and observing whether the pathogen carries specific mutations at drug-resistance sites. This advancement has led to the collati...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2658-z
更新日期:2019-02-08 00:00:00
abstract:BACKGROUND:The landscape of biological and biomedical research is being changed rapidly with the invention of microarrays which enables simultaneous view on the transcription levels of a huge number of genes across different experimental conditions or time points. Using microarray data sets, clustering algorithms have ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-27
更新日期:2009-01-20 00:00:00
abstract:BACKGROUND:The most common method of identifying groups of functionally related genes in microarray data is to apply a clustering algorithm. However, it is impossible to determine which clustering algorithm is most appropriate to apply, and it is difficult to verify the results of any algorithm due to the lack of a gol...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-115
更新日期:2005-05-12 00:00:00
abstract:BACKGROUND:Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq and microarray are two main technologies for profiling gene expression levels. However, considerable discrepancy has been found between DEGs detected using the t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0847-y
更新日期:2016-01-11 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:The imputation of genotypes increases the power of genome-wide association studies. However, the imputation quality should be assessed in each particular case. Nevertheless, not all imputation softwares control the error of output, e.g., the last release of fastPHASE program (1.4.8) lacks such an option. In ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03589-0
更新日期:2020-07-24 00:00:00
abstract:BACKGROUND:The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in significant conflict with the plurality signal is a frequent task in comparative genomics, and especially ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-123
更新日期:2012-06-07 00:00:00
abstract:BACKGROUND:Whole exome sequencing (WES) has become the strategy of choice to identify a coding allelic variant for a rare human monogenic disorder. This approach is a revolution in medical genetics history, impacting both fundamental research, and diagnostic methods leading to personalized medicine. A plethora of effic...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S14-S9
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Inference of sequence homology is inherently an evolutionary question, dependent upon evolutionary divergence. However, the insertion and deletion penalties in the most widely used methods for inferring homology by sequence alignment, including BLAST and profile hidden Markov models (profile HMMs), are not b...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0832-5
更新日期:2015-12-10 00:00:00
abstract:BACKGROUND:Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0592-2
更新日期:2015-05-13 00:00:00
abstract:BACKGROUND:We present the algorithm PFClust (Parameter Free Clustering), which is able automatically to cluster data and identify a suitable number of clusters to group them into without requiring any parameters to be specified by the user. The algorithm partitions a dataset into a number of clusters that share some co...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-213
更新日期:2013-07-03 00:00:00
abstract:BACKGROUND:The definition of a distance measure plays a key role in the evaluation of different clustering solutions of gene expression profiles. In this empirical study we compare different clustering solutions when using the Mutual Information (MI) measure versus the use of the well known Euclidean distance and Pears...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-111
更新日期:2007-03-30 00:00:00
abstract:BACKGROUND:Microarray has been widely used to measure the gene expression level on the genome scale in the current decade. Many algorithms have been developed to reconstruct gene regulatory networks based on microarray data. Unfortunately, most of these models and algorithms focus on global properties of the expression...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S11-S15
更新日期:2010-12-14 00:00:00
abstract:BACKGROUND:Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-508
更新日期:2010-10-12 00:00:00
abstract:BACKGROUND:Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole-cell scale. In such representations, the cell is considered as a system composed of interlocked sub...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03637-9
更新日期:2020-07-23 00:00:00
abstract:BACKGROUND:Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1419-5
更新日期:2017-01-03 00:00:00
abstract:BACKGROUND:Inferring gene regulatory network (GRN) has been an important topic in Bioinformatics. Many computational methods infer the GRN from high-throughput expression data. Due to the presence of time delays in the regulatory relationships, High-Order Dynamic Bayesian Network (HO-DBN) is a good model of GRN. Howeve...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0823-6
更新日期:2015-11-25 00:00:00
abstract:BACKGROUND:Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between species and groups of species, and classical matrices such as those in the BLOSUM series fail to ac...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-457
更新日期:2011-11-24 00:00:00
abstract:BACKGROUND:In microarray experiments the numbers of replicates are often limited due to factors such as cost, availability of sample or poor hybridization. There are currently few choices for the analysis of a pair of microarrays where N = 1 in each condition. In this paper, we demonstrate the effectiveness of a new al...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-489
更新日期:2008-11-21 00:00:00