One of the grad students and I continue to struggle with finding the best way to represent her results.
The results take the form of gel images - autoradiograms of positions of bands in the gel, representing the sizes of radioactive RNA fragments. But which kinds of bands convey significant information depends on the enzyme that's been used and on the pattern seen in the 'ladder' (unfolded RNA, the control) lane. But the images of the gels are too complex for the reader to make sense of without a lot of effort, and we present a typical one only to reassure the reader that the analysis was competently done. Thus we need to develop a representation that summarizes the gel results.
Sometimes the presence of a band in the 'structure' (folded RNA, the test) lane is significant information, telling us that the folding of the RNA lets the enzyme cut at a place that it couldn't in the unfolded RNA. Other times (different position or different enzyme) the presence of a band tells us nothing. Sometimes the absence of a band tells us that the folding makes that part of the RNA inaccessible, but sometimes it is just because that enzyme can't ever cut at that kind of position. To make matters worse, the gel results, though reasonably reproducible, are not always exactly the same, probably due to slight and unavoidable fluctuations in temperatures and volume measurements.
So we want our representation to convey both positive information and lack of information. One representation needs to say "These bases of the RNA have this cutting pattern with this enzyme, and these other bases have that pattern" and another needs to say "These bases of the RNA have this structure and these other bases have that pattern".
We're still working on it.
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3 weeks ago in Genomics, Medicine, and Pseudoscience
Can you just take a picture and annotate with an editor like Paint?
ReplyDeleteWe do this for thin layer chromatography data. For example see this pic taken from this experiment.
I am finding it a bit hard to visualise the data itself, but could you have a table as follows?: -
ReplyDelete(1) each row is a position along the DNA from (-) to (+) past the transcription start
(2) each column is a different bit of info for that site, derived from a different enzyme e.g. No info, or "double-stranded" or "single-stranded"
(3) a summary column next to the info columns with "double stranded", "Single-Stranded" or "ambiguous"
Then as the next figure project an image of what that data might mean in terms of the secondary structure of the DNA.
This sounds too simplistic so I guess I haven't grasped the extent of the problem, but I would really like to see the data and what you hope to do to present it.
The paper's figures will include a representative annotated gel photo, but these are complex and their interpretation relies on subtle comparisons. (more complex than this: http://jvi.asm.org/cgi/content/full/73/2/1165/F3) There can be more than 100 bands in each gel lane, but only some of these carry relevant information. Sometimes a darker control band means the nucleotide is base-paired, sometimes it means the nucleotide is not base-paired (depending on the RNase enzyme used).
ReplyDeleteInterpretation is also complicated by variation between replicate gels. We've done enough replicates that we're confident of the conclusions, but we don't want to drag the reader through a band-by-band analysis of all the bands on all the gels.