User talk:Foleyha/sandbox

Topic Peer Review 1
Under Discovery title - 2nd and 3rd sentences do not seem to belong there. Under Evolutionary History title I would suggest removing "in a article" and start with "the lab concluded"MLibrarian (talk) 22:06, 10 October 2017 (UTC)

Reply PR 1
Thank you for the feedback. We will be sure to do extensive editing. The history section is just notes and has not been written out properly yet. Foleyha (talk) 02:07, 23 October 2017 (UTC)

Topic Peer Review 2
I really like the new graphic - it is great! If you made it yourself - this is fantastic! If not, please cite. Maybe you could find a way to keep the original figure in the text? The Contents tab is very thoughtful! I would suggest the following changes in the text: 1) The sentence "The TATA box was first identified in 1978 by American biochemist David Hogness and his lab.[1]" in the second paragraph seems not to belong there. It is a part of history and in fact is repeated in the history. I would just remove it from there. 2) the sentence "Is a promoter located immediately upstream of the start site of transcription. It contains a consensus DNA sequence TATAAA called the Hogness-Goldberg box (or TATA box)." does not belong in History tab but would seem better in the 2nd paragraph in the Introduction part 3) In Sequence and Prevalence[edit] "The TATA box is a component of the eukaryotic core promotor" - shall be "promoter" 4) In Sequence and Prevalence The word promoter is used many times but only once it is linked to another Wiki page, I suggest add interlinks to all "promoter"MLibrarian (talk) 18:25, 17 October 2017 (UTC)

Reply PR 2
The figures are the original work of luttysar and we decided to replace the original figure because it was giving examples of pribnow box sequences, which are actually something different than TATA boxes. In response to 3), the eukaryotic core promoter is an actual thing and is more specific than promoter. There is not a page that specifically describes the eukaryotic core promoter to link to however. Foleyha (talk) 02:07, 23 October 2017 (UTC)

Review Opinion 1
The overall form of the article entry is good. However, I think the editors should leave the original figure in their modified article (the figure that introduces different types of promoter sequences containing TATA).

In addition, the “discovery” section can be expanded. The editors can add some information about the discovery of TATA promoter sequences in different types of organisms. — Preceding unsigned comment added by Tanxt (talk • contribs) 01:45, 24 October 2017 (UTC)

Reply RO 1
We decided to replace the original figure because it was giving examples of pribnow box sequences, which are actually something different than TATA boxes. This is specific to prokaryotes. We will expand the organism description with regards to specific eukaryotes. Luttysar (talk) 20:30, 27 October 2017 (UTC)

Review Opinion 2
I would add TBP in parentheses after you first mention the TATA Binding Protein in the first line of the “Evolutionary History” section, so it is clear that they are the same.

1. Maybe take out the sentence about who discovered the TATA box in the the intro paragraph and just say it was discovered in 1978, that way you do not basically have the same sentence twice. 2. Maybe add a diagram to the mutation section because they are very useful in the other sections. 3. In the second paragraph of “Role in Transcription” you can remove the statement about TFIID being a transcription factor as it has already been stated in the previous paragraph. 4. If possible, expand on the medical conditions mentioned at the end of the article

Review Opinion 3
I think the introductory paragraph could have a better flow to it and clarify specifically for a non-expert reader what the TATA box is and why it is important. I think you made it clear on what it is, but maybe just plainly state why it is important. You could also just add one or two words clarifying what a histone (and other specific terms) is, for example, to allow non-readers to easily flow through your paragraph.

In your introductory paragraph, I noticed that you changed the sentence that says "and vice versa) and is involved in the process" to "...histone and vice versa), or involved in the process". Is this really an "or"? I was thinking it would still be an "and" since it is also involved in the process of transcription--just a thought.

I think your figure 1 is helpful to see the overall picture of where the TATA box is located relatively, and I think that it definitely adds to your information. Figure 2 also paints a clear picture as to what your information says.

I think your group made a significant contribution to this Wiki page. Your paragraph headings gave structure and ease in finding desired information, and your references are complete. My main suggestion would be to clarify some words in the introductory paragraph that gives a good idea of what the TATA box is and purpose for a non-expert reader. — Preceding unsigned comment added by Tanxt (talk • contribs) 01:54, 24 October 2017 (UTC)

Review Opinion 4
Overall, I like this wiki page -- everything is clearly expressed, organized, and impressively intuitive. However, I think there are some points that could be done better:

1. When I read “Evolutionary History” part, I was confused by term “TBP” because I don’t really know what does this abbreviation stand for and there is no link associated with this “TBP”. If the potential readers of this wiki page are basically everyone who is interested in, I believe they will get confused by this "TBP" as well. Therefore, this page will be more reader-friendly if you could edit “TBP” by explaining more about this term or adding a related wiki link.

2. From my view, the “History” part should only contain the content which is related with the main concept, which is "TATA box"; therefore, I don’t think "analogous sequence" is an appropriate sub-section of "history" section.

3. In "Sequence & Prevalence" section, it will be better to add 5’ and 3’ to define the sequence of Saccharomyces genomes (TATA(A/T)A(A/T)(A/G).

4. The figures used in this wiki page are intuitive and really help to understand the content. However, I noticed that that these figures and words are not complementary. Words and figures are both good, what missed here is a linker to bring these two things together. For example, the presence of Fig.1 in "Introduction" part doesn’t make any sense because in "introduction", you don't talk about "upstream enhancer", "promoter sequence", which are key words I noticed in Fig.1. Therefore, Fig.1 is a little bit confused to me at the beginning. However, as I read the second paragraph of “sequence and prevalence” part, I realized that Fig.1 is the illustration of that specific paragraph. Thus, by adding a "see Fig.2" in second paragraph of “sequence and prevalence” part or moving the position of Fig.1 from introduction part to “sequence and prevalence” part, you make readers' life much easier.

5. More information could be added to introduction. Since you did a great work in illustrating the idea of TATA box from different perspective, the core ideas could be summarized and added to expand the introduction part. — Preceding unsigned comment added by Tanxt (talk • contribs) 03:30, 24 October 2017 (UTC)

Reply RO 4
Text organization and content changes have been made as needed. The introduction has been given introductory thoughts on the sections to come. Luttysar (talk) 14:34, 2 November 2017 (UTC)

Nils' Comments
Nice job! Make sure to link to as many existing articles as possible and be as inclusive of existing work as possible; I like your mechanistic discussion - keep going!

Gillian's Comments
Great job and I like the new figures! I think adding a figure like the one from the original wikipedia, that shows TATA sequence examples would be helpful to include (which sounds like something you are already considering).