Abstract：
:The interpretation of data-driven experiments in genomics often involves a search for biological categories that are enriched for the responder genes identified by the experiments. However, knowledge bases such as the Gene Ontology (GO) contain hundreds or thousands of categories with very high overlap between categories. Thus, enrichment analysis performed on one category at a time frequently returns large numbers of correlated categories, leaving the choice of the most relevant ones to the user's; interpretation. Here we present model-based gene set analysis (MGSA) that analyzes all categories at once by embedding them in a Bayesian network, in which gene response is modeled as a function of the activation of biological categories. Probabilistic inference is used to identify the active categories. The Bayesian modeling approach naturally takes category overlap into account and avoids the need for multiple testing corrections met in single-category enrichment analysis. On simulated data, MGSA identifies active categories with up to 95% precision at a recall of 20% for moderate settings of noise, leading to a 10-fold precision improvement over single-category statistical enrichment analysis. Application to a gene expression data set in yeast demonstrates that the method provides high-level, summarized views of core biological processes and correctly eliminates confounding associations.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Bauer S,Gagneur J,Robinson PNdoi
10.1093/nar/gkq045subject
Has Abstractpub_date
2010-06-01 00:00:00pages
3523-32issue
11eissn
0305-1048issn
1362-4962pii
gkq045journal_volume
38pub_type
杂志文章abstract：:In order to study the effects of DNA structure on cellular processes such as transcription, we have made a series of plasmids that locate several different kinds of DNA structure (stiff, flexible or curved) near the sites of cleavage by commonly-used restriction enzymes. One can use these plasmids to place any DNA reg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.22.9447
更新日期：1989-11-25 00:00:00
abstract：:DNA topoisomerases and DNA site-specific recombinases are biologically important enzymes involved in a diverse set of cellular processes. We show that replacement of a phosphodiester linkage by a 5'-bridging phosphorothioate linkage creates an efficient suicide substrate for calf thymus topoisomerase I and lambda inte...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.15.2973
更新日期：1995-08-11 00:00:00
abstract：:In many eukaryotic mRNAs one or more short 'upstream' open reading frames, uORFs, precede the initiator of the main coding sequence. Upstream ORFs are functionally diverse as illustrated by their variety of features in polyamine pathway biosynthetic mRNAs. Their propensity to act as sensors for regulatory circuits and...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkp1037
更新日期：2010-01-01 00:00:00
abstract：:The thermal stabilities of the duplexes formed between 4'-thio-modified oligodeoxynucleotides and their DNA and RNA complementary strands were determined and compared with those of the corresponding unmodified oligodeoxynucleotides. A 16mer oligodeoxynucleotide containing 10 contiguous 4'-thiothymidylate modifications...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.21.4117
更新日期：1996-11-01 00:00:00
abstract：:'Linker scanning' has been used as an efficient method for systematically surveying a segment of DNA for functional elements by mutagenesis. A three-step PCR method was developed to simplify this process. In this method, a set of 'mutation primers' was made with 6 to 8 base substitutions in the center of the primers. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.16.3745
更新日期：1993-08-11 00:00:00
abstract：:The DNA damage response is vigorously activated by DNA double-strand breaks (DSBs). The chief mobilizer of the DSB response is the ATM protein kinase. We discovered that the COP9 signalosome (CSN) is a crucial player in the DSB response and an ATM target. CSN is a protein complex that regulates the activity of cullin ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv270
更新日期：2015-05-19 00:00:00
abstract：:MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular compartments--namely MNXref--and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1117
更新日期：2016-01-04 00:00:00
abstract：:Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1074
更新日期：2012-01-01 00:00:00
abstract：:The disappearance of defined restriction fragments of the beta 1-globin, an albumin and the A1 vitellogenin gene was quantitated after DNase I digestion and expressed by a sensitivity factor defined by a mathematical model. Analysis of naked DNA showed that the gene fragments have similar but not identical sensitivity...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.11.2455
更新日期：1981-06-11 00:00:00
abstract：:The proportion of cytosines methylated in the DNA of nucleosome oligomers and of core particles appears indistinguishable from that of total nuclear DNA from CHO cells. However the DNA in nucleoprotein which is initially released from nuclei by treatment with very low levels of micrococcal nuclease and the first 10% o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.9.3097
更新日期：1977-09-01 00:00:00
abstract：:Two of the tRNA's found in rabbit reticulocytes are substrates for a post-transcriptional modification leading to the incorporation of guanine into the polynucleotide chain. The major guanylated tRNA was previously identified as tRNA (His). In the present report we show that the minor guanylated tRNA is tRNA (Asn), an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.10.2521
更新日期：1976-10-01 00:00:00
abstract：:The APOBEC3 proteins are unique to mammals. Many inhibit retrovirus infection through a cDNA cytosine deamination mechanism. HIV-1 neutralizes this host defense through Vif, which triggers APOBEC3 ubiquitination and degradation. Here, we report an APOBEC3F-like, double deaminase domain protein from three artiodactyls:...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl721
更新日期：2006-01-01 00:00:00
abstract：:The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.1.303
更新日期：1999-01-01 00:00:00
abstract：:Aedes aegypti mosquitoes vector several arboviruses of global health significance, including dengue viruses and chikungunya virus. RNA interference (RNAi) plays an important role in antiviral immunity, gene regulation and protection from transposable elements. Double-stranded RNA binding proteins (dsRBPs) are importan...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv152
更新日期：2015-04-20 00:00:00
abstract：:Human Hepatitis B Virus (HBV) RNAs contain a cis -acting sequence, the post-transcriptional regulatory element (HPRE), which facilitates the cytoplasmic localization of intronless transcripts. Our previous studies have shown that the HPRE is composed of at least two independent sub-elements, HPREalpha and HPREbeta, wh...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.21.4818
更新日期：1998-11-01 00:00:00
abstract：:We have examined the replication patterns of ribosomal DNA plasmids in vivo and in vitro using Xenopus eggs. Plasmids carrying different parts of the Xenopus ribosomal DNA sequence were allowed to replicate either in vitro in an egg extract or in vivo after microinjection into unfertilized eggs. The replication interm...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.7.1463
更新日期：1992-04-11 00:00:00
abstract：:The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1089
更新日期：2017-01-04 00:00:00
abstract：:Inability of T7 RNA polymerase to processively transcribe higher eukaryotic chromatin is interpreted as a correlate of its reported inhibition by nucleosomes on reconstituted templates in vitro . We used chromosomally integrated reporter cassettes to examine features of T7 transcription in a lower eukaryotic system. L...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.20.4626
更新日期：1998-10-15 00:00:00
abstract：:The effect of different levels of mercury substitution on the rate and extent of hybridisation of globin mRNA with a complementary DNA (cDNA) copy has been investigated. It was found that mercuration significantly reduces both the rate of hybridisation and the extent of the reaction, but that these effects are abolish...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.8.2357
更新日期：1979-12-20 00:00:00
abstract：:Reverse gyrase is a peculiar DNA topoisomerase, specific of hyperthermophilic Archaea and Bacteria, which has the unique ability of introducing positive supercoiling into DNA molecules. Although the function of the enzyme has not been established directly, it has been suggested to be involved in DNA protection and rep...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl115
更新日期：2006-04-14 00:00:00
abstract：:The human immunodeficiency virus (HIV) and other retroviruses show extensive genomic variation, which is primarily due to error-prone replication by the viral reverse transcriptase (RT) enzymes. RT errors include misincorporation with subsequent extension of the mismatched terminal base, and extension of realigned pri...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.8.1319
更新日期：1995-04-25 00:00:00
abstract：:High-throughput screening assays have been developed to rapidly identify small molecule inhibitors targeting catalytic group I introns. Biochemical reactions catalyzed by a self-splicing group I intron derived from Pneumocystis carinii or from bacteriophage T4 have been investigated. In vitro biochemical assays amenab...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.24.5051
更新日期：1996-12-15 00:00:00
abstract：:The hammerhead self-cleaving motif occurs in a variety of RNAs that infect plants and consists of three non-conserved helices connected by a highly conserved central core. A variant hammerhead, called the extended hammerhead, is found in satellite 2 transcripts from a variety of caudate amphibians. The extended hammer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.11.2189
更新日期：1997-06-01 00:00:00
abstract：:MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1139
更新日期：2018-01-04 00:00:00
abstract：:The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1044
更新日期：2012-01-01 00:00:00
abstract：:Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of hig...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq808
更新日期：2011-02-01 00:00:00
abstract：:The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.23.4698
更新日期：2000-12-01 00:00:00
abstract：:The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1163
更新日期：2015-01-01 00:00:00
abstract：:There are a few algorithms designed to solve the problem of the optimal alignment of one sequence, the pattern, of length m, with another, longer sequence the text, of length n. These algorithms allow mismatches, deletions and insertions. Algorithms to date run in O(mn) time. Let us define an integer, k, which is the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.1.31
更新日期：1986-01-10 00:00:00
abstract：:A simple, reproducible affinity chromatography method has been adapted for separation of high molecular weight supercoiled circular molecules from mammalian cells. Electron microscopic analysis of EB viral DNA obtained by this method, from the non-producer Burkitt's lymphoma line Raji, revealed monomer-sized viral mol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.24.10345
更新日期：1987-12-23 00:00:00
