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 annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kelder T,van Iersel MP,Hanspers K,Kutmon M,Conklin BR,Evelo CT,Pico ARdoi
10.1093/nar/gkr1074subject
Has Abstractpub_date
2012-01-01 00:00:00pages
D1301-7issue
Database issueeissn
0305-1048issn
1362-4962pii
gkr1074journal_volume
40pub_type
杂志文章abstract::The dicistrovirus intergenic internal ribosome entry site (IGR IRES) directly recruits the ribosome and initiates translation using a non-AUG codon. A subset of IGR IRESs initiates translation in either of two overlapping open reading frames (ORFs), resulting in expression of the 0 frame viral structural polyprotein a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku622
更新日期:2014-08-01 00:00:00
abstract::The Chinese hamster cell line, DC-3F, is heterozygous at the DHFR locus, and each allele can be distinguished on the basis of a unique DNA restriction pattern, protein isoelectric profile and in the abundancy of the DHFR mRNAs it expresses. Although each allele produces four transcripts, 1000, 1650 and 2150 nucleotide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.24.6597
更新日期:1992-12-25 00:00:00
abstract::Genomes undergo changes in organization as a result of gene duplications, chromosomal rearrangements and local mutations, among other mechanisms. In contrast to prokaryotes, in which genes of a common function are often organized in operons and reside contiguously along the genome, most eukaryotes show much weaker clu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku667
更新日期:2014-09-01 00:00:00
abstract::In Trypanosoma brucei the genes are organised into long polycistronic transcription units and only three promoters for protein-encoding genes and a single terminator have been characterised. These promoters recruit a polI-like RNA polymerase for the transcription units encoding the two major stage-specific antigens of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.2.597
更新日期:2000-01-15 00:00:00
abstract::Hexokinase 2 is an essential factor for signalling repression through the Saccharomyces cerevisiae high-glucose sensing pathway. The main regulatory mechanism that controls the HXK2 gene expression in yeast is mediated by the Rgt1 and Med8 transcription factors, which repress HXK2 expression in low-glucose containing ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl028
更新日期:2006-03-09 00:00:00
abstract::Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein-protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq481
更新日期:2010-07-01 00:00:00
abstract::The -1 ribosomal frameshifting requires the existence of an in cis RNA slippery sequence and is promoted by a downstream stimulator RNA. An atypical RNA pseudoknot with an extra stem formed by complementary sequences within loop 2 of an H-type pseudoknot is characterized in the severe acute respiratory syndrome corona...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki731
更新日期:2005-07-29 00:00:00
abstract::The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz344
更新日期:2019-07-09 00:00:00
abstract::DNA polymerases alpha and delta are essential enzymes believed to play critical roles in initiation and replication of chromosome DNA. In this study, we show that the genes for Schizosaccharomyces pombe (S.pombe) DNA polymerase alpha and delta (pol alpha+ and pol delta+) are essential for cell viability. Disruption of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.16.3821
更新日期:1993-08-11 00:00:00
abstract::Apolipoprotein B (apoB) is a major protein component of low density and very low density lipoproteins. Because of its large size and heterogeneity, molecular studies of apoB have been difficult, and its structure and regulation remain poorly understood. We now report the identification of human apoB cDNA clones by ant...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.19.6937
更新日期:1985-10-11 00:00:00
abstract::We characterized and purified a protein from rat liver which specifically binds to a DNA motif present in a liver-specific enhancer of the rat tyrosine aminotransferase (TAT) gene, when offered as single-stranded DNA. Binding is highly sequence-specific and coincides with a region known to be essential for function of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.6.1243
更新日期:1992-03-25 00:00:00
abstract::Chloroplast DNA, isolated from a synchronized culture of Chlamydomonas reinhardii, was digested with restriction endonucleases and examined in the electron microscope. Restriction fragments containing displacement loops (D-loop) were photographed and measured to determine the position of replicated sequences in relati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.9.3843
更新日期:1984-05-11 00:00:00
abstract::Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classificat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1111
更新日期:2018-01-04 00:00:00
abstract::Activating sequence factor 1 (ASF-1) is a nuclear DNA-binding activity that is found in monocots and dicots. It interacts with several TGACG-containing elements that have been characterized from viral and T-DNA genes, the prototypes of which are the as-1 element of the CaMV 35S promoter and the ocs element from the oc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.18.3778
更新日期:1995-09-25 00:00:00
abstract::The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli RR1 strain carrying the eco57IRM genes on a recombinant plasmid. The molecular weight of the denaturated methylase is 63 kDa. The restriction endonuclease exists in a monomeric form with an apparent molecular weight of 104-1...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.22.6043
更新日期:1992-11-25 00:00:00
abstract::Repair of DNA double-strand breaks (DSBs) with homologous chromosomes is a hallmark of meiosis that is mediated by recombination 'bridges' between homolog axes. This process requires cooperation of DMC1 and RAD51 to promote homology search and strand exchange. The mechanism(s) regulating DMC1/RAD51-ssDNA nucleoprotein...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa406
更新日期:2020-07-09 00:00:00
abstract::The crp gene of E. coli, which codes for cAMP receptor protein (CRP), has been cloned in the plasmid pBR322 on the basis of a genetic complementation. One of the recombinant plasmids, pHA1, was shown to direct the synthesis of CRP in a cell-free system. The location of the crp gene was determined by constructing subcl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.4.1345
更新日期:1982-02-25 00:00:00
abstract::Two DNA polymerases have been purified from the 105,000 x g supernatant of ungerminated wheat. The purification stages included: high speed centrifugation, salt fractionation, DEAE-cellulose chromatography, Sephadex G-150 filtration and phosphocellulose chromatography. Several properties of the two enzyme (called A an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.11.2077
更新日期:1975-11-01 00:00:00
abstract::Alfalfa mosaic virus RNA 4, the subgenomic messenger for viral coat protein, was partially digested with RNase T1 or RNase A and the sequence of a number of fragments was deduced by in vitro labeling with polynucleotide kinase and application of RNA sequencing techniques. From overlapping fragments, the complete prima...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.10.2213
更新日期:1980-05-24 00:00:00
abstract::Topoisomerases catalyse changes in the topological state of DNA and are required for many aspects of DNA metabolism. While the functions of topoisomerases I and II in eukaryotes are well established, the role of topoisomerase III remains poorly defined. We have identified a gene in the fission yeast Schizosaccharomyce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.20.4050
更新日期:1999-10-15 00:00:00
abstract::A tetradecanucleotide U-A-G-C(U-C-G)2G-G-C-Up corresponding to bases 21-34 of a nascent sequence of formylmethionyl tRNA of E. coli has been synthesized by the joining of two combinations of chemically synthesized oligonucleotides: 1) U-A-G-C + U-C-G-U-C-G + G-G-C-Up and 2) U-A-G-C + U-C-G-U + C-G-G-G-C-Up. In reactio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.17.3909
更新日期:1980-09-11 00:00:00
abstract::Recent effective use of TAL Effectors (TALEs) has provided an important approach to the design and synthesis of sequence-specific DNA-binding proteins. However, it is still a challenging task to design and manufacture effective TALE modulators because of the limited knowledge of TALE-DNA interactions. Here we synthesi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku535
更新日期:2014-08-01 00:00:00
abstract::Chromatin boundaries regulate gene expression by modulating enhancer-promoter interactions and insulating transcriptional influences from organized chromatin. However, mechanistic distinctions between these two aspects of boundary function are not well understood. Here we show that SF1, a chromatin boundary located in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp362
更新日期:2009-07-01 00:00:00
abstract::Every bulky lesion in DNA can potentially inhibit the Taq DNA polymerase and thereby decrease the amplification produced in the polymerase chain reaction. We investigated the feasibility of using this inhibition to quantify DNA lesions produced by the anticancer drug cisplatin. Products were detected by electrophoresi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.22.6209
更新日期:1991-11-25 00:00:00
abstract::Chromatin fragments released from intact Friend erythroleukemia cell nuclei during limited incubation with micrococcal nuclease, DNase II or DNase I were analyzed to determine the distribution of DNA methyltransferase in chromatin. The enzyme was released in a free form when internucleosomal DNA was digested with micr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.20.5359
更新日期:1981-10-24 00:00:00
abstract::We have previously reported that transcription from a distal promoter (promoter B) of the estrogen receptor alpha (ERalpha) gene is responsible for the increased expression of ERalpha in human breast carcinomas. This paper first characterized the promoter B region in terms of transient transfection experiments with lu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.3.903
更新日期:1999-02-01 00:00:00
abstract::Single-nucleotide polymorphisms (SNPs) are often linked to critical phenotypes such as diseases or responses to vaccines, medications and environmental factors. However, the specific molecular mechanisms by which a causal SNP acts is usually not obvious. Changes in RNA secondary structure emerge as a possible explanat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1009
更新日期:2013-01-07 00:00:00
abstract::Structures of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 have been determined by NMR spectroscopy under low salt conditions. All protons and phosphorus nuclei resonances have been assigned. Signals of H5'/5" have been assigned stereospecifically. All 3JH,H and 3JP,H coupling constants have been measured. The structures were dete...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.22.4589
更新日期:1997-11-15 00:00:00
abstract::HeLa cell OTF-1 has been purified on the basis of its DNA binding activity and used to raise a polyclonal rabbit antiserum. This antiserum is shown to recognize both native and denatured OTF-1 from both human and a similar protein from Xenopus culture cells, but to react either more weakly or not at all with the lymph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.5.1845
更新日期:1989-03-11 00:00:00
abstract::The RosettaDesign server identifies low energy amino acid sequences for target protein structures (http://rosettadesign.med.unc.edu). The client provides the backbone coordinates of the target structure and specifies which residues to design. The server returns to the client the sequences, coordinates and energies of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl163
更新日期:2006-07-01 00:00:00