https://ecoliwiki.org/colipedia/api.php?action=feedcontributions&feedformat=atom&user=65.55.209.35EcoliWiki - User contributions [en]2026-11-04T18:11:27ZUser contributionsMediaWiki 1.43.11https://ecoliwiki.org/colipedia/index.php?title=PMID:12368244&diff=186564PMID:123682442007-07-28T23:12:25Z<p>65.55.209.35: New PMID: Page!</p>
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<span style = 'font-size: large'> '''McCue, LA, Thompson, W, Carmack, CS and Lawrence, CE''' (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison.''Genome Res.'' '''12''':1523-32</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || As the number of sequenced genomes has grown, the questions of which species are most useful and how many genomes are sufficient for comparison have become increasingly important for comparative genomics studies. We have systematically addressed these questions with respect to phylogenetic footprinting of transcription factor (TF) binding sites in the gamma-proteobacteria, and have evaluated the statistical significance of our motif predictions. We used a study set of 166 Escherichia coli genes that have experimentally identified TF binding sites upstream of the gene, with orthologous data from nine additional gamma-proteobacteria for phylogenetic footprinting. Just three species were sufficient for approximately 74.0% of the motif predictions to correspond to the experimentally reported E. coli sites, and important characteristics to consider when choosing species were phylogenetic distance, genome size, and natural habitat. We also performed simulations using randomized data to determine the critical maximum a posteriori probability (MAP) values for statistical significance of our motif predictions (P = 0.05). Approximately 60% of motif predictions containing sites from just three species had average MAP values above these critical MAP values. The inclusion of a species very closely related to E. coli increased the number of statistically significant motif predictions, despite substantially increasing the critical MAP value.<br />
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12368244 PubMed]<br />
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==References==<br />
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<references/></div>65.55.209.35https://ecoliwiki.org/colipedia/index.php?title=PMID:15980584&diff=147663PMID:159805842007-07-26T10:24:51Z<p>65.55.209.35: New PMID: Page!</p>
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<span style = 'font-size: large'> '''Maier, H, Döhr, S, Grote, K, O'Keeffe, S, Werner, T, Hrabé de Angelis, M and Schneider, R''' (2005) LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts.''Nucleic Acids Res.'' '''33''':W779-82</span><br />
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|{{TableHeadingColor}} |'''Abstract''' || The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). Owing to the limitations (no direction, unverified automatic prediction) of the co-occurrence approach, the primary data in the LitMiner database represent postulated basic gene-gene relationships. The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modelling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. LitMiner (http://andromeda.gsf.de/litminer) and WikiGene (http://andromeda.gsf.de/wiki) can be used unrestricted with any Internet browser.<br />
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15980584 PubMed]<br />
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<references/></div>65.55.209.35