Abstract：
:Discovering which regulatory proteins, especially transcription factors (TFs), are active under certain experimental conditions and identifying the corresponding binding motifs is essential for understanding the regulatory circuits that control cellular programs. The experimental methods used for this purpose are laborious. Computational methods have been proven extremely effective in identifying TF-binding motifs (TFBMs). In this article, we propose a novel computational method called MotifExpress for discovering active TFBMs. Unlike existing methods, which either use only DNA sequence information or integrate sequence information with a single-sample measurement of gene expression, MotifExpress integrates DNA sequence information with gene expression measured in multiple samples. By selecting TFBMs that are significantly associated with gene expression, we can identify active TFBMs under specific experimental conditions and thus provide clues for the construction of regulatory networks. Compared with existing methods, MotifExpress substantially reduces the number of spurious results. Statistically, MotifExpress uses a penalized multivariate regression approach with a composite absolute penalty, which is highly stable and can effectively find the globally optimal set of active motifs. We demonstrate the excellent performance of MotifExpress by applying it to synthetic data and real examples of Saccharomyces cerevisiae. MotifExpress is available at http://www.stat.illinois.edu/~pingma/MotifExpress.htm.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zamdborg L,Ma Pdoi
10.1093/nar/gkp554subject
Has Abstractpub_date
2009-09-01 00:00:00pages
5246-54issue
16eissn
0305-1048issn
1362-4962pii
gkp554journal_volume
37pub_type
杂志文章abstract：:RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Non...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky486
更新日期：2018-09-19 00:00:00
abstract：:DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx385
更新日期：2017-07-03 00:00:00
abstract：:The beta-globin gene of a patient with mRNA-deficient beta o-thalassemia has been sequenced. We find a single nucleotide deletion in amino acid codon 44 that produces a UGA terminator at codon 60. We have previously shown that the beta-globin mRNA of this patient is correctly spliced and polyadenylated, but rapidly tu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.18.5421
更新日期：1982-09-25 00:00:00
abstract：:The -175 T greater than C mutation in the promoter of the A gamma- or G gamma-globin gene causes a 50-100 fold increase of the expression of the respective gene in adult erythroid cells (Hereditary Persistence of Fetal Hemoglobin). We show here that this mutation increases 3-9 fold the expression of a gamma-CAT report...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.14.5509
更新日期：1989-07-25 00:00:00
abstract：:Several cDNA clones were isolated from cDNA libraries constructed with mRNA longer than 28S RNA from the murine cell line PYS-2/12. The plasmids have inserts containing 1-1.2 kb of the ribosomal 5' external transcribed spacer followed by nearly 700 nt of sequence for 18S rRNA and ending with a B2 element (retroposon)....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.4.671
更新日期：1992-02-25 00:00:00
abstract：:RNase J is a conserved ribonuclease that belongs to the β-CASP family of nucleases. It possesses both endo- and exo-ribonuclease activities, which play a key role in pre-rRNA maturation and mRNA decay. Here we report high-resolution crystal structures of Deinococcus radiodurans RNase J complexed with RNA or uridine 5'...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv444
更新日期：2015-06-23 00:00:00
abstract：:We have sequenced the external transcribed spacer (ETS) of a ribosomal transcription unit from Xenopus laevis, together with sections of the preceding non-transcribed spacer. Our analysis was carried out on the same cloned transcription unit as that from which the internal transcribed spacers (ITS) were previously seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.7.2387
更新日期：1982-04-10 00:00:00
abstract：:A DNA region of 2750 base pairs encompassing the genes III, VI and I of bacteriophage M13 has been sequenced by the Maxam-Gilbert procedure. By establishing the nucleotide changes introduced by several amber mutations, the coding region and the regulatory signals of each gene have been deduced. The genes appear to spa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.8.2799
更新日期：1979-06-25 00:00:00
abstract：:The transcription of ribosomal genes in a cell line (Kc) derived from female D.melanogaster, has been investigated using hybridization probes prepared from restriction fragments of a cloned rDNA repeat with a 5 kb type I [Wellauer et al. (1978) Cell 14, 269-278] intron. Gels, of nuclear RNA that have been transferred ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.1.67
更新日期：1980-01-11 00:00:00
abstract：:DNA polymerase (Pol) beta null mouse embryonic fibroblasts provide a useful cell system to investigate the effects of alterations in base excision repair (BER) on genome stability. These cells are characterized by hypersensitivity to the cytotoxic effects of methyl methanesulfonate (MMS) and by decreased repair of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki168
更新日期：2005-01-12 00:00:00
abstract：:Unlike short interfering RNAs (siRNAs), which are commonly designed to repress a single messenger RNA (mRNA) target through perfect base pairing, microRNAs (miRNAs) are endogenous small RNAs that have evolved to concurrently repress multiple mRNA targets through imperfect complementarity. MicroRNA target recognition i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku171
更新日期：2014-05-01 00:00:00
abstract：:GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly returns relevant Re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks448
更新日期：2012-07-01 00:00:00
abstract：:We studied fluorescence intensity, polarization and lifetime of some commonly used fluorophores conjugated to oligodeoxyribonucleotides with different primary and secondary structures. We found that fluorescence intensity can increase or decrease upon hybridization of the labeled strand to its complement depending on ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.9.2089
更新日期：2002-05-01 00:00:00
abstract：:Telomerase is a ribonucleoprotein reverse transcriptase that synthesizes and maintains telomeric DNA. Studies of telomeres and telomerase are facilitated by the large number of linear DNA molecules found in ciliated protozoa, such as Tetrahymena thermophila. To examine the expression of telomerase, we investigated the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.21.4269
更新日期：1999-11-01 00:00:00
abstract：:Establishment and differentiation of mammary alveoli during pregnancy are controlled by prolactin through the transcription factors STAT5A and STAT5B (STAT5), which also regulate temporal activation of mammary signature genes. This study addressed the question whether the methyltransferase and transcriptional co-activ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv776
更新日期：2015-10-15 00:00:00
abstract：:The initial genomic response to serum growth factors is the transcriptional activation of a set of immediate-early genes. Serum-induced transcriptional activation of several of these genes involves the formation of a ternary complex that includes the serum response factor (SRF), a 62 kDa ternary complex factor (TCF) a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.7.1345
更新日期：1996-04-01 00:00:00
abstract：:Cortical development is controlled by transcriptional programs, which are orchestrated by transcription factors. Yet, stable inheritance of spatio-temporal activity of factors influencing cell fate and localization in different layers is only partly understood. Here we find that deletion of Dot1l in the murine telence...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky953
更新日期：2019-01-10 00:00:00
abstract：:The growing application of gene expression profiling demands powerful yet user-friendly bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first released in 2014 to address the key need for interpreting gene expression data within the context of protein-protein interaction (PPI) netwo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz240
更新日期：2019-07-02 00:00:00
abstract：:Bacterial Hfq is a protein that plays an important role in the regulation of genes in cooperation with sRNAs. Escherichia coli Hfq (EcHfq) has two or more sites that bind RNA(s) including U-rich and/or the poly(A) tail of mRNA. However, functional and structural information about Bacillus subtilis Hfq (BsHfq) includin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr892
更新日期：2012-02-01 00:00:00
abstract：:The double helix is known to form as a result of hybridization of complementary nucleic acid strands in aqueous solution. In the helix the negatively charged phosphate groups of each nucleic acid strand are distributed helically on the outside of the duplex and are available for interaction with cationic groups. Catio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.14.3051
更新日期：2001-07-15 00:00:00
abstract：:More than 20 different heterogeneous nuclear ribonucleoproteins (hnRNPs) are associated with pre-mRNAs in the nucleus of mammalian cells and these proteins appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. The arrangement of hnRNP proteins on pre-mRNAs is likely to be unique f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.6.1059
更新日期：1994-03-25 00:00:00
abstract：:Protein-RNA interactions in small nuclear ribonucleoproteins (UsnRNPs) from HeLa cells were investigated by irradiation of purified nucleoplasmic snRNPs U1 to U6 with UV light at 254 nm. The cross-linked proteins were analyzed on one- and two-dimensional gel electrophoresis systems, and the existence of a stable cross...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.23.10985
更新日期：1988-12-09 00:00:00
abstract：:The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.1.22
更新日期：2001-01-01 00:00:00
abstract：:Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these. The database has hierarchical classifications in which homologous sets of peptidases a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr987
更新日期：2012-01-01 00:00:00
abstract：:The occurrence of DNA tracts of the three binary base combinations: R.Y, K.M and W;S has been mapped in the complete genomes of Haemophilus influenzae and Escherichia coli. A highly significant over-representation of W tracts is observed in both bacteria. The excess of W tracts is particularly striking in the 10% inte...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.22.4491
更新日期：1999-11-15 00:00:00
abstract：:Loading of the replicative ring helicase onto the origin of replication (oriC) is the final outcome of a well coordinated series of events that collectively constitute a primosomal cascade. Once the ring helicase is loaded, it recruits the primase and signals the switch to the polymerization mode. The transient nature...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh628
更新日期：2004-06-01 00:00:00
abstract：:The Xist lncRNA requires Repeat A, a conserved RNA element located in its 5' end, to induce gene silencing during X-chromosome inactivation. Intriguingly, Repeat A is also required for production of Xist. While silencing by Repeat A requires the protein SPEN, how Repeat A promotes Xist production remains unclear. We r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa789
更新日期：2020-10-09 00:00:00
abstract：:We have established a sensitive, monoclonal antibody (Mab)-based procedure permitting the selective enrichment of sequences containing the miscoding alkylation product O6-ethylguanine (O6-EtGua) from mammalian DNA. H5 rat hepatoma cells were reacted with the N-nitroso carcinogen N-ethyl-N-nitrosourea in vitro, to give...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.16.4467
更新日期：1991-08-25 00:00:00
abstract：:The binding of anti poly(I). poly (C) Fab fragments to double or triple stranded polynucletides has been studied by fluorescence. Association constants were deduced from competition experiments. The comparison of the association constants leads to the conclusion that several atoms of the base residues do not interact ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.12.3337
更新日期：1976-12-01 00:00:00
abstract：:Using cyanoethyldiisopropylamino phosphoramidite chemistry, four oligonucleotides constituting a part of the sequence of the initiator t-RNA from B. subtilis were synthesized. For the protection of the exocyclic amino functions of bases, phenoxyacetyl group was used for adenine and guanine, and acetyl group was prefer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.18.7381
更新日期：1989-09-25 00:00:00
