Abstract:
BACKGROUND:Identification of transcription factors (TFs) responsible for modulation of differentially expressed genes is a key step in deducing gene regulatory pathways. Most current methods identify TFs by searching for presence of DNA binding motifs in the promoter regions of co-regulated genes. However, this strategy may not always be useful as presence of a motif does not necessarily imply a regulatory role. Conversely, motif presence may not be required for a TF to regulate a set of genes. Therefore, it is imperative to include functional (biochemical and molecular) associations, such as those found in the biomedical literature, into algorithms for identification of putative regulatory TFs that might be explicitly or implicitly linked to the genes under investigation. RESULTS:In this study, we present a Latent Semantic Indexing (LSI) based text mining approach for identification and ranking of putative regulatory TFs from microarray derived differentially expressed genes (DEGs). Two LSI models were built using different term weighting schemes to devise pair-wise similarities between 21,027 mouse genes annotated in the Entrez Gene repository. Amongst these genes, 433 were designated TFs in the TRANSFAC database. The LSI derived TF-to-gene similarities were used to calculate TF literature enrichment p-values and rank the TFs for a given set of genes. We evaluated our approach using five different publicly available microarray datasets focusing on TFs Rel, Stat6, Ddit3, Stat5 and Nfic. In addition, for each of the datasets, we constructed gold standard TFs known to be functionally relevant to the study in question. Receiver Operating Characteristics (ROC) curves showed that the log-entropy LSI model outperformed the tf-normal LSI model and a benchmark co-occurrence based method for four out of five datasets, as well as motif searching approaches, in identifying putative TFs. CONCLUSIONS:Our results suggest that our LSI based text mining approach can complement existing approaches used in systems biology research to decipher gene regulatory networks by providing putative lists of ranked TFs that might be explicitly or implicitly associated with sets of DEGs derived from microarray experiments. In addition, unlike motif searching approaches, LSI based approaches can reveal TFs that may indirectly regulate genes.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Roy S,Heinrich K,Phan V,Berry MW,Homayouni Rdoi
10.1186/1471-2105-12-S10-S19subject
Has Abstractpub_date
2011-10-18 00:00:00pages
S19issn
1471-2105pii
1471-2105-12-S10-S19journal_volume
12 Suppl 10pub_type
杂志文章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:High-throughput technology allows for genome-wide measurements at different molecular levels for the same patient, e.g. single nucleotide polymorphisms (SNPs) and gene expression. Correspondingly, it might be beneficial to also integrate complementary information from different molecular levels when building...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1183-6
更新日期:2016-08-30 00:00:00
abstract:BACKGROUND:Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The wide usage of protein sequence analysis in par with the growth of databases signifies the importance...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-127
更新日期:2004-09-09 00:00:00
abstract:BACKGROUND:determining beforehand specific positions to align (anchor points) has proved valuable for the accuracy of automated multiple sequence alignment (MSA) software. This feature can be used manually to include biological expertise, or automatically, usually by pairwise similarity searches. Multiple local similar...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-445
更新日期:2010-09-02 00:00:00
abstract:BACKGROUND:Scaffold proteins are known for being crucial regulators of various cellular functions by assembling multiple proteins involved in signaling and metabolic pathways. Identification of scaffold proteins and the study of their molecular mechanisms can open a new aspect of cellular systemic regulation and the re...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1079-5
更新日期:2016-07-28 00:00:00
abstract:BACKGROUND:HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins. RESULTS:We developed a single-instructi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3019-7
更新日期:2019-09-14 00:00:00
abstract:BACKGROUND:Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-260
更新日期:2005-10-19 00:00:00
abstract:BACKGROUND:The main research topic in this paper is how to compare multiple biological experiments using transcriptome data, where each experiment is measured and designed to compare control and treated samples. Comparison of multiple biological experiments is usually performed in terms of the number of DEGs in an arbi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3302-7
更新日期:2019-12-27 00:00:00
abstract:BACKGROUND:Cross-platform analysis of gene express data requires multiple, intricate processes at different layers with various platforms. However, existing tools handle only a single platform and are not flexible enough to support custom changes, which arise from the new statistical methods, updated versions of refere...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-75
更新日期:2011-03-17 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:Dystrophinopathy is one of the most common human monogenic diseases which results in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Mutations in the dystrophin gene are responsible for both DMD and BMD. However, the clinical phenotypes and treatments are quite different in these two m...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1504-4
更新日期:2017-02-02 00:00:00
abstract:BACKGROUND:As a consequence of the evolutionary process, data collected from related species tend to be similar. This similarity by descent can obscure subtler signals in the data such as the evidence of constraint on variation due to shared selective pressures. In comparative sequence analysis, for example, sequence s...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-222
更新日期:2007-06-26 00:00:00
abstract:BACKGROUND:The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association studies which identify genetic determinants of pathogen virulence and drug...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2580-9
更新日期:2019-01-07 00:00:00
abstract:BACKGROUND:Joint and individual variation explained (JIVE), distinct and common simultaneous component analysis (DISCO) and O2-PLS, a two-block (X-Y) latent variable regression method with an integral OSC filter can all be used for the integrated analysis of multiple data sets and decompose them in three terms: a low(e...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1037-2
更新日期:2016-06-06 00:00:00
abstract:BACKGROUND:Although many of the genic features in Mycobacterium abscessus have been fully validated, a comprehensive understanding of the regulatory elements remains lacking. Moreover, there is little understanding of how the organism regulates its transcriptomic profile, enabling cells to survive in hostile environmen...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3042-8
更新日期:2019-09-10 00:00:00
abstract:BACKGROUND:Prioritizing disease genes is trying to identify potential disease causing genes for a given phenotype, which can be applied to reveal the inherited basis of human diseases and facilitate drug development. Our motivation is inspired by label propagation algorithm and the false positive protein-protein intera...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2040-6
更新日期:2018-02-08 00:00:00
abstract:BACKGROUND:Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC) molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-132
更新日期:2005-05-31 00:00:00
abstract:BACKGROUND:Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-198
更新日期:2005-08-05 00:00:00
abstract:BACKGROUND:S-glutathionylation is the formation of disulfide bonds between the tripeptide glutathione and cysteine residues of the protein, protecting them from irreversible oxidation and in some cases causing change in their functions. Regulatory glutathionylation of proteins is a controllable and reversible process a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03571-w
更新日期:2020-09-14 00:00:00
abstract:BACKGROUND:High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key for drawing meaningful and accurate conclusions from the massive and complex datasets generat...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-94
更新日期:2010-02-18 00:00:00
abstract:BACKGROUND:The main goal of the whole transcriptome analysis is to correctly identify all expressed transcripts within a specific cell/tissue--at a particular stage and condition--to determine their structures and to measure their abundances. RNA-seq data promise to allow identification and quantification of transcript...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-135
更新日期:2014-05-09 00:00:00
abstract:BACKGROUND:Multidimensional protein identification technology (MudPIT)-based shot-gun proteomics has been proven to be an effective platform for functional proteomics. In particular, the various sample preparation methods and bioinformatics tools can be integrated to improve the proteomics platform for applications lik...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S15-S8
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Protein-protein docking, which aims to predict the structure of a protein-protein complex from its unbound components, remains an unresolved challenge in structural bioinformatics. An important step is the ranking of docked poses using a scoring function, for which many methods have been developed. There is ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-286
更新日期:2013-10-01 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: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:The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1870-y
更新日期:2017-11-15 00:00:00
abstract::We developed a new computational technique called Step-Level Differential Response (SLDR) to identify genetic regulatory relationships. Our technique takes advantages of functional genomics data for the same species under different perturbation conditions, therefore complementary to current popular computational techn...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S11-S1
更新日期:2014-01-01 00:00:00
abstract::Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughp...
journal_title:BMC bioinformatics
pub_type: 杂志文章,评审
doi:10.1186/1471-2105-13-S16-S4
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further proc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-249
更新日期:2005-10-13 00:00:00
abstract:BACKGROUND:N-linked protein glycosylation plays an important role in various biological processes, including protein folding and trafficking, and cell adhesion and signaling. The acquisition of a novel N-glycosylation site may have significant effect on protein structure and function, and therefore, on the phenotype. ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0468-5
更新日期:2015-01-28 00:00:00