Abstract:
BACKGROUND:Increasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue types to improve statistical power especially in trans-eQTL mapping. Meta-analysis framework is also necessary for ChrX eQTL discovery. RESULTS:We developed a novel tool, meta-eqtl, for fast eQTL meta-analysis of arbitrary sample size and arbitrary number of datasets. Further, this tool accommodates versatile modeling, eg. non-parametric model and mixed effect models. In addition, meta-eqtl readily handles calculation of chrX eQTLs. CONCLUSIONS:We demonstrated and validated meta-eqtl as fast and comprehensive tool to meta-analyze multiple datasets and ChrX eQTL discovery. Meta-eqtl is a set of command line utilities written in R, with some computationally intensive parts written in C. The software runs on Linux platforms and is designed to intelligently adapt to high performance computing (HPC) cluster. We applied the novel tool to liver and adipose tissue data, and revealed eSNPs underlying diabetes GWAS loci.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Di Narzo AF,Cheng H,Lu J,Hao Kdoi
10.1186/s12859-014-0392-0subject
Has Abstractpub_date
2014-11-28 00:00:00pages
392issn
1471-2105pii
s12859-014-0392-0journal_volume
15pub_type
杂志文章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:In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Golm Metabolome Database for metabolite data (GMD) represents one such effort to make these data broadl...
journal_title:BMC bioinformatics
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doi:10.1186/1471-2105-8-216
更新日期:2007-06-23 00:00:00
abstract:BACKGROUND:The information in large collections of phylogenetic trees is useful for many comparative genomic studies. Therefore, there is a need for flexible tools that allow exploration of such collections in order to retrieve relevant data as quickly as possible. RESULTS:In this paper, we present TPMS (Tree Pattern-...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-109
更新日期:2013-03-27 00:00:00
abstract:BACKGROUND:Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methylation, especially N6-methyladenosine, has become one of the most researched topics in epigenetics. ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2840-3
更新日期:2019-05-02 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:Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various existing methods measure similarity between two profiles and, hence, the likelihood that the two prote...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S4-S7
更新日期:2007-05-22 00:00:00
abstract:BACKGROUND:Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, integrative analysis have been performed by using genomics, transcriptomics, epigenomics, proteomics an...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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abstract:BACKGROUND:Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation analysis. This study ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2005-11-23 00:00:00
abstract:BACKGROUND:High-throughput screens comparing growth rates of arrays of distinct micro-organism cultures on solid agar are useful, rapid methods of quantifying genetic interactions. Growth rate is an informative phenotype which can be estimated by measuring cell densities at one or more times after inoculation. Precise ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2010-05-28 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0357-3
更新日期:2014-11-19 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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abstract:BACKGROUND:High throughput DNA/RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3015-y
更新日期:2019-08-15 00:00:00
abstract:BACKGROUND:Light microscopy is of central importance in cell biology. The recent introduction of automated high content screening has expanded this technology towards automation of experiments and performing large scale perturbation assays. Nevertheless, evaluation of microscopy data continues to be a bottleneck in man...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-30
更新日期:2010-01-14 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
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-32
更新日期:2005-02-17 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2019-03-14 00:00:00
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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
abstract:BACKGROUND:Many methods for species tree inference require data from a sufficiently large sample of genomic loci in order to produce accurate estimates. However, few studies have attempted to use analytical theory to quantify "sufficiently large". RESULTS:Using the multispecies coalescent model, we report a general an...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1266-4
更新日期:2016-11-11 00:00:00
abstract:BACKGROUND:Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. In order to fully capture the intrinsic value and knowledge expressed within them, we need to take advantage of their inner structure, which implicitly co...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-265
更新日期:2012-10-15 00:00:00
abstract:BACKGROUND:Several features are known to correlate with the GC-content in the human genome, including recombination rate, gene density and distance to telomere. However, by testing for pairwise correlation only, it is impossible to distinguish direct associations from indirect ones and to distinguish between causes and...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2009-01-30 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2005-12-07 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-55
更新日期:2004-05-07 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-537
更新日期:2010-10-29 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S1-S3
更新日期:2007-03-08 00:00:00
abstract:BACKGROUND:Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a phylogeny. Changes between homologous characters are typically modell...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2018-09-21 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2016-07-28 00:00:00
abstract:BACKGROUND:Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0887-y
更新日期:2016-01-20 00:00:00
abstract:BACKGROUND:Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure compariso...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2010-03-17 00:00:00
abstract:BACKGROUND:Next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output. Even a low error rate can cause a large number of errors due to the high number of nucleotides being sequenced. Identifying sequencing errors fr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2013-12-18 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1963-7
更新日期:2017-12-28 00:00:00