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Collating articles associated to latently expressed TF genes, we used a simple text-mining approach to group TF genes by previous research (see Additional file 8).
The SRL is an interesting way for designing systematic reviews, as we are focusing at identifying, evaluating, and comparing available published articles associated to a particular topic area of interest for answering a specific scientific question.
NCBI's built-in links between Pubmed records and genes were used to retrieve articles associated to human, mouse or rat orthologues of the gene of interest, and keywords embedded in Pubmed's MeSH terms served to associate Pubmed records with diseases.
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Data in this article are associated to the research articles "Methylation Landscape of Human Breast Cancer Cells in Response to Dietary Compound Resveratrol".
To account for the tree structure of MeSH, for each MeSH term associated with an article, the article is considered associated to all of the parent terms of that MeSH term.
About 18 797 (65.3%) genes are associated to articles which have 100 or fewer genes linked to them.
Table 1 shows the distribution of mutations associated to articles in each database.
A link to PubMed articles associated with the compound via depositor-provided cross-references is displayed under the Depositor Provided PubMed Citations section, and a link to those associated with the compound via common MeSH annotations is shown under the NLM Curated PubMed Citations section.
Another relation is (iii) "of WordNet" that connects articles associated with WordNet classes to an appropriate entity type.
Our results demonstrate that only a small fraction of the curated mutations are available from the narrative part of the articles, and that most of the information is available only in tables and supplementary files associated to the articles.
Only two community-chosen terms associated to two articles were judged to be too specific by curators.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com