Additional file 1: of TIGERi: modeling and visualizing the responses to perturbation of a transcription factor network

Supplementary Text and Figures. (DOC 7227 kb

Studies characteristics in trypanosomiasis: parasite species, experimental infection models and aims of the studies.

<p>Studies characteristics in trypanosomiasis: parasite species, experimental infection models and aims of the studies.</p

Study selection process for <i>Trypanosoma</i> studies.

<p>Study selection process for <i>Trypanosoma</i> studies.</p

Checklist for the reporting of <i>Trypanosoma</i> experiments.

<p>Checklist for the reporting of <i>Trypanosoma</i> experiments.</p

Linear correlation (A) and Bland-Altman (B) plots between scores of method reporting in <i>Trypanosoma</i> experiments.

<p>Evaluation based strictly on what was explicitly included in the published paper (Evaluator 1) and on interpretations and assumptions determined by an expert in the field (Evaluator 2).</p

Diagram of articles about Trypanosomiasis[MeSH] published between 2000 and 2012.

<p>Number of articles published per journal (black bars) and the percentage of methods reporting (red bars). The figure shows that the quality of method reporting is not related with the number of papers published by any one of the journals.</p

Venn diagram summarising the quality of methods reporting in the three domains of <i>Trypanosoma</i> experiments.

<p>The average and range of percentages scored of the quality of methods reporting is shown in brackets.</p

Scatter plots between the reported information in <i>Trypanosoma</i> experiments and year of publication.

<p>The figure shows that there is no correlation [<i>p</i> = 0.711] and that between 2000 and 2012 the quality of methods reporting has remain constant (arithmetic mean  = 65.5%).</p

Scatter plots showing the relationship between the quality of methods reporting and the bibliometric indices.

<p>Journal impact factor in which the papers were published (A), h-index of the corresponding author (B), and number of citations that the articles have received in other publications (C). Spearman's rank correlation coefficient <i>r</i> is shown alongside the regression lines. The figure shows that there is no correlation between the quality of methods reporting and impact factor [<i>r</i> = −0.04, <i>p</i> = 0.868]. A similar result is shown with h-index, which was searched using the full name of the corresponding author [<i>r</i> = −0.12, <i>p</i> = 0.593; continuous line] and then filtered by the topic Trypanosom* [<i>r</i> = −0.21, <i>p</i> = 0.345; broken line]. There is a weak but significant correlation between the quality of methods reporting and the number of citations recorded by Google Scholar [<i>r</i> = −0.42, <i>p</i> = 0.044; broken line], but not by Web of Science [<i>r</i> = −0.35, <i>p</i> = 0.105; continuous line]. In order to find out if this association is due to a causal effect of the time of publication, a correlation between the number of citations and the time of publication was done (D), and also a weak but significant correlation was shown with the records of Web of Science [<i>r</i> = 0.42, <i>p</i> = 0.046; continuous line], but not with Google Scholar [<i>r</i> = 0.40, <i>p</i> = 0.057; broken line].</p

Comparison of SNPs identified after mapping with BWA and Bowtie.

<p>Gene regions are from the gene start to the gene end and include introns.</p