Abstract:
:Mutations help us to understand the molecular origins of diseases. Researchers, therefore, both publish and seek disease-relevant mutations in public databases and in scientific literature, e.g. Medline. The retrieval tends to be time-consuming and incomplete. Automated screening of the literature is more efficient. We developed extraction methods (called MEMA) that scan Medline abstracts for mutations. MEMA identified 24,351 singleton mutations in conjunction with a HUGO gene name out of 16,728 abstracts. From a sample of 100 abstracts we estimated the recall for the identification of mutation-gene pairs to 35% at a precision of 93%. Recall for the mutation detection alone was >67% with a precision rate of >96%. This shows that our system produces reliable data. The subset consisting of protein sequence mutations (PSMs) from MEMA was compared to the entries in OMIM (20,503 entries versus 6699, respectively). We found 1826 PSM-gene pairs to be in common to both datasets (cross-validated). This is 27% of all PSM-gene pairs in OMIM and 91% of those pairs from OMIM which co-occur in at least one Medline abstract. We conclude that Medline covers a large portion of the mutations known to OMIM. Another large portion could be artificially produced mutations from mutagenesis experiments. Access to the database of extracted mutation-gene pairs is available through the web pages of the EBI (refer to http://www.ebi. ac.uk/rebholz/index.html).
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Rebholz-Schuhmann D,Marcel S,Albert S,Tolle R,Casari G,Kirsch Hdoi
10.1093/nar/gkh162keywords:
subject
Has Abstractpub_date
2004-01-02 00:00:00pages
135-42issue
1eissn
0305-1048issn
1362-4962pii
32/1/135journal_volume
32pub_type
杂志文章abstract::The role of TATA elements in the expression of a mammalian promoter was investigated in the fission yeast Schizosaccharomyces pombe, by studying the human adenovirus E2-early promoter. This is a unique dual promoter with two nonconsensus TATA elements directing transcription from two cap sites, +1 and -26. A sequence ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.11.2737
更新日期:1993-06-11 00:00:00
abstract::Secondary structure-sensitive chemical and enzymatic probes have been used to produce a model for the folding of the last 68 residues of the 3'-non-coding region of beet necrotic yellow vein benevirus RNA 3. The structure consists of two stem-loops separated by a single-stranded region. RNA 3-derived transcripts were ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.23.4723
更新日期:1997-12-01 00:00:00
abstract::A peculiar phenomenon is observed in several adenovirus type 2 or 5 (Ad2 or Ad5) transformed cell lines: the right hand and left hand terminal regions of the viral genome present in the viral DNA insertions of these cell lines are found to be linked together. A large part of the viral DNA insertion present in the Ad5 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.7.2189
更新日期:1982-04-10 00:00:00
abstract::IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku939
更新日期:2014-11-10 00:00:00
abstract::A stable conformer of Escherichia coli tRNA(Glu), obtained in the absence of Mg(2+), is inactive in the aminoacylation reaction. Probing it with diethylpyrocarbonate, dimethyl sulfate and ribonuclease V1 revealed that it has a hairpin structure with two internal loops; the helical segments at both extremities have the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.17.3583
更新日期:1999-09-01 00:00:00
abstract::The rDNA cluster in Saccharomyces cerevisiae is located 450 kb from the left end and 610 kb from the right end of chromosome XII and consists of approximately 150 tandemly repeated copies of a 9.1 kb rDNA unit. To explore the biological significance of this specific chromosomal context, chromosome XII was split at bot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl293
更新日期:2006-05-31 00:00:00
abstract::Currently transgenic frog embryos are generated using restriction-enzyme-mediated integration (REMI) on decondensed sperm nuclei followed by nuclear transplantation into unfertilized eggs. We have developed a simplified version of this protocol that has the potential to increase the numbers of normally developing tran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.4.e12
更新日期:2000-02-15 00:00:00
abstract::Alternative splicing (AS) of pre-mRNAs is an important regulatory mechanism shaping the transcriptome. In plants, only few RNA-binding proteins are known to affect AS. Here, we show that the glycine-rich RNA-binding protein AtGRP7 influences AS in Arabidopsis thaliana. Using a high-resolution RT-PCR-based AS panel, we...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks873
更新日期:2012-12-01 00:00:00
abstract::Distamycin binds the minor groove of duplex DNA at AT-rich regions and has been a valuable probe of protein interactions with double-stranded DNA. We find that distamycin can also inhibit protein interactions with G-quadruplex (G4) DNA, a stable four-stranded structure in which the repeating unit is a G-quartet. Using...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg392
更新日期:2003-06-01 00:00:00
abstract::New transcripts generated by RNA polymerase II (RNAPII) are generally processed in order to form mature mRNAs. Two key processing steps include a precise cleavage within the 3' end of the pre-mRNA, and the subsequent polymerization of adenosines to produce the poly(A) tail. In yeast, these two functions are performed ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx674
更新日期:2017-09-29 00:00:00
abstract::Laser-Raman spectra of poly(rI) show the formation of an ordered complex in aqueous solutions of high ionic strength. This structure exhibits the A-helix geometry, contains stacked bases and is apparently stabilized by specific hydrogen bonding involving hypoxanthine C6=0 groups. Thermal dissociation of the poly(rI) c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.7.2407
更新日期:1977-07-01 00:00:00
abstract::The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1154
更新日期:2018-01-04 00:00:00
abstract::We describe a novel 3'-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2'-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1293
更新日期:2011-03-01 00:00:00
abstract::How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz176
更新日期:2019-06-20 00:00:00
abstract::The effect of UV-irradiation on the conversion of the single-stranded DNA of the parvovirus Minute-Virus-of-Mice (MVM) to duplex Replicative Forms (RF) was studied after infection of mouse A9 fibroblasts. UV-irradiation of the virus prior to infection of unirradiated cells resulted in a dose-dependent, single-hit, inh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.8.2577
更新日期:1982-04-24 00:00:00
abstract::Mitome is a specialized mitochondrial genome database designed for easy comparative analysis of various features of metazoan mitochondrial genomes such as base frequency, A+T skew, codon usage and gene arrangement pattern. A particular function of the database is the automatic reconstruction of phylogenetic relationsh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm763
更新日期:2008-01-01 00:00:00
abstract::Extracts of the human glioma cell line A1235 (lacking O(6)-methylguanine-DNA methyltransferase) are known to restore a G:T mismatch to a normal G:C pair in a G:T-containing model (45 bp) DNA substrate. Herein we demonstrate that substitution of G:T with O(6)-methylguanine:T (m6G:T) results in extract-induced intra-str...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.11.2409
更新日期:2001-06-01 00:00:00
abstract::Mitochondrial DNA is a sensitive target of chemical carcinogens (Backer and Weinstein (1980) Science 209, 297-299), suggesting that mutations of the mitochondrial genome occur in tumor cells. We examined this point by comparing mitochondrial DNA sequences in four rat tumors with those of normal rat liver. Some novel m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.6.1635
更新日期:1983-03-25 00:00:00
abstract::We present MultiGO, a web-enabled tool for the identification of biologically relevant gene sets from hierarchically clustered gene expression trees (http://ekhidna.biocenter.helsinki.fi/poxo/multigo). High-throughput gene expression measuring techniques, such as microarrays, are nowadays often used to monitor the exp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl694
更新日期:2006-01-01 00:00:00
abstract::An examination, using reversed-phase chromatography and cyanogen bromide treatment, of tRNATyr, tRNAHis, tRNAAsn, and tRNAAsp from SV40-transformed mouse fibroblasts grown to different cell densities, untransformed cells grown to confluence, and mouse liver indicates that: (1) The tissue cultured mouse fibroblasts exa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.7.2513
更新日期:1978-07-01 00:00:00
abstract::The generalized mismatch repair system of Streptococcus pneumoniae (the Hex system) can eliminate base pair mismatches arising in heteroduplex DNA during transformation or by DNA polymerase errors during replication. Mismatch repair is most likely initiated at nicks or gaps. The present work was started to examine the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.20.5525
更新日期:1991-10-25 00:00:00
abstract::In small oocytes of Xenopus species, two sets of 5S RNA genes, oocyte-type and somatic-type, are fully activated. The 5S RNA transcripts are temporarily stored, half in association with TFIIIA to form a 7S particle, the other half in association with tRNA and two proteins (p48 and p43) to form a 42S particle. It has b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.21.8679
更新日期:1987-11-11 00:00:00
abstract::Guanine-quadruplexes (G4) consist of non-canonical four-stranded helical arrangements of guanine-rich nucleic acid sequences. The bulky and thermodynamically stable features of G4 structures have been shown in many respects to affect normal nucleic acid metabolism. In vivo conversion of G4 structures to single-strande...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr630
更新日期:2011-11-01 00:00:00
abstract::The gene encoding myelin basic protein (MBP) contains multiple activator sequences spanning upstream of its transcriptional initiation site which differentially promote transcription in glial cells. The proximal activator sequence, designated MB1, activates transcription in a glial cell type specific manner. This sequ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.3.545
更新日期:1992-02-11 00:00:00
abstract::When the function of origins of replication in yeast was compromised by placing ARS sequences downstream of strong promoters, ARS activity might have been affected either by transcription or by an altered chromatin configuration induced by the construct. To distinguish between these possibilities, derivatives of the y...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.19.3904
更新日期:1994-09-25 00:00:00
abstract::During erythropoiesis in the chick, the nucleosome repeat length increases from 190 base pairs to 212 base pairs. This increase is correlated with a dramatic increase in the concentration of the red cell specific histone H5 (from 0.2 molecules per nucleosome to 1 molecule per nucleosome) and with no change in the conc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.4.1179
更新日期:1978-04-01 00:00:00
abstract::Spirochetes of the genus Borrelia possess unusual genomes that consist in a linear chromosome and multiple linear and circular plasmids. The linear replicons are terminated by covalently closed hairpin ends, referred to as hairpin telomeres. The hairpin telomeres represent a simple solution to the end-replication prob...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw344
更新日期:2016-06-20 00:00:00
abstract::Starting from a crude E. coli extract, two activities which specifically protect highly repetitive bacterial DNA sequences (called PU for Palindromic Unit or REP for Repetitive Extragenic Palindromic sequence) against a digestion with Exonuclease III have been purified. We show that one of these activities is due to t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.13.3941
更新日期:1990-07-11 00:00:00
abstract::The hypoxanthine-guanine phosphoribosyltransferase (HGPRT) enzyme of Trypanosoma brucei and related parasites provides a rational target for the treatment of African sleeping sickness and several other parasitic diseases. To characterize the T. brucei HGPRT enzyme in detail, the T. brucei hgprt was isolated within a 4...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.23.5431
更新日期:1993-11-25 00:00:00
abstract::Polyketide synthases (PKSs) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. Bioinformatics analysis of sequence and structural features of PKS proteins plays a crucial role in discovery of new natural products by genome mining, as well as in design of novel secondary meta...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq340
更新日期:2010-07-01 00:00:00