Comparison of Published and Photocopied Figures

<p>Example of an image that, when seen in color (A), is rich with information; much of this information is lost when it is photocopied by students (B), as when the original is held on reserve in the library, as is required for subscription-based journals, or is provided via interlibrary loan. This image of a developing fly embryo was labeled to reveal bands of differentially expressed proteins, with HAIRY in red, KRüPPEL in green, and GIANT in blue. (Image courtesy of Stephen W. Paddock, Jim Langeland, and Sean Carroll at the University of Wisconsin–Madison.)</p

Example of Student's Data Mining for Exam Question

<p>Figure 2 from <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020145#pbio-0020145-Bozdech1" target="_blank">Bozdech et al. (2003)</a> showing the gene expression profiles for 12 groups of genes expressed at different stages of <i>Plasmodium</i> life cycle inside red blood cells. Genomics students were asked to summarize this figure as a part of a take-home exam.</p

Venn diagrams of gene predictions.

<p>(A) The diagram to the left shows the number of predicted protein coding genes that share stop sites with the other annotations. Overlapping regions indicate genes having same stop site between annotations. (B) The diagram to the right shows the number of predicted protein coding genes that share start site and stop site with the other annotations. Overlapping regions indicate genes having exact matches between annotations.</p

Summary of wet-lab results.

<p>We incubated <i>H. utahensis</i> for seven days in GSL-2 medium with various macromolecular substrates. The topmost row lists the macromolecular substrates used as carbon sources. The first nine entries in the leftmost column indicate the substrates used for enzyme assays. Plus signs denote the level of activity, ranging in order of lowest to highest from 0 to +++.</p

Glycolysis/gluconeogenesis pathway.

<p>Diagram based on RAST's KEGG pathway map displays present and absent enzymes for <i>H. utahensis</i>. Green boxes indicate that the enzyme was predicted by RAST and displayed in the KEGG map. Yellow boxes designate enzymes that were called by RAST but had not been added to the KEGG map. Red boxes mark enzymes that were listed as absent and could not be located in the <i>H. utahensis</i> genome.</p

Comparison of putative glycoside hydrolase start sites.

<p>Examination of an individual gene displays tendencies of the annotation services. RAST identifies GTG as the start codon for the gene, while IMG and JCVI select two ATG codons at different locations. Predicted start codon affects gene length.</p

Comparison of rRNA calls.

<p>Review of predicted coding regions for ribosomal RNA for each annotation service shows that IMG and RAST have identical calls, while JCVI fails to call 23s rRNA and predicts different start and stop sites.</p

Potential comparison tool.

<p>Hypothetical comparison of start sites from multiple annotations, combined with species-specific RBS data. Start #2 would be the most likely start codon based on RBS spacing.</p

Comparison of start codons.

<p>Analysis of predicted protein coding genes displays incidence of ATG and alternative start codons for each annotation. RAST has a greater tendency to call genes with alternative start codons than the other annotation services.</p

<i>H. utahensis</i> primary contig and ORC/Cdc6 genes.

<p>Circular display of the largest contig of the <i>H. utahensis</i> genome sequence. The contig begins at the top and wraps clockwise. The red bars illustrate the location of ORC/Cdc6 orthologs. The ORC/Cdc6 gene numbered 3 lies near the origin of replication, at 2,327,225 base pairs.</p