Talk:Researching SNPs TSD

Well structured page again that yields a great amount of details like the comparison of substitution values from different amino acids. I also really liked your approach of comparing the importance of the different SNP-positions against the number of occurrence of each of these positions in all the databases (depicted in figure 4). --Joerdensv 8:55, 12 June 2012 (UTC)

Hi, just a quick question about HGMD:

• "Synonymous SNPs however are not recorded." Are you sure about that? It lists a His-His mutation for HFE. --Bernhoferm 13:35, 10 June 2012 (UTC)
  • Nevermind... "If such mutations are known to adversely affect mRNA splicing or gene expression, or have been reported in significant association with disease, they may be included." Guess that's the case for us.
    • Interesting, in our case they indeed do not appear in HGMD, although by this definition [1] V324V might apply -jonas

Feedback:

Your wiki is really well structured and readable. I liked the detailed descriptions of the databases (while not being too long). Though maybe a list of the actual SNPs for HEXA found in the different databases would be nice, not just the statistics. Below I gave you a list of possible corrections. There are still some TODOs in you wiki, so I guess I'll check in again later. --Bernhoferm 18:04, 11 June 2012 (UTC)

• By now it should be done. We will add another figure with the SNPs highlighted in the structure later but apart from that nothing big should change anymore. Sorry for the delay -jonas
• Do you really think a list for every database is necessary..... I believe the joint results are important and from the single databases the numbers are enough -ali

Corrections?:

• In the first section you talk about the nt sequence being 117 nt longer at the beginning and then "Since this region is annotated to belong to an exon, the question remains whether this has an effect on the protein sequence." -- Did you mean "intron"? If it was within an exon wouldn't it be certain to affect the protein sequence?
  • It really is supposed to be 'exon'. I also wondered and assume that this is due to the fact the our protein undergoes several precursor stages and this part is later cleaved off (after all there is no indication that this is the final, mature mRNA) -jonas
• "The mutation in context of the number of database a mutation is present on this position are depicted in Figure 4" -- What? :P
  • Hopefully clearer now ;) -jonas
    • Come on..... it was not so bad
• "Overall near all of the 5 highlighted residues there is a accumulation of known SNPs." -- Maybe you should switch the two halfs of this sentence. Also the 'a' should be 'an'. -> "Overall there is an accumulation of known SNPs near all of the 5 highlighted residues."
  • Thanks, the sentence needed to be slightly redesigned anyway, it should be clearer now -jonas
    • maybe you can also find some weird sentences from jonas for a change, mr corrector...
• Table 1 might be missing its "index" (don't know if it is on purpose). -> "Table 1: Overview of result overlaps"
  • For whatever reason the cross-references extension only autonumbers figures, not Tables, so we have to hardcode it at the end when we know how many Tables we will have. It is included now -jonas
• "...and by the filter check box on the web page the results can be specified." -- I think "...with the filter..." would be better.
  • I want to point out explicitly that the user has to click around rather than being able to use the search syntax directly
• "The authors wish to be recused from the judgement of SNPdbe due to a possible conflict of interest." -- I don't know if "recused" is the proper word (in this passive sense). Maybe "excused"?
  • Seems correct to me? http://www.answers.com/topic/recuse -jonas
    • As joint research with bernhoferm made clear: be recused is correct, however the term seems to only apply to judges, so I'll change it ;) -jonas