Question: Is the database, 'Yeast Nucleosome Atlas (YNA)', reliable?
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gravatar for parsiabasimfar
2.4 years ago by
parsiabasimfar0 wrote:

I am working on a project to explore histone modification discrepancies (such as lysine methylation or acetylation) between two sets of genes in the budding yeast s. cerevisiae.

The database, Yeast Nucleosome Atlas, has drawn data from several articles (Pokholok 2005 for example), which have conveyed Chip-chip studies. In the original articles data are represented by reporting relative nucleosome occupancy vs H3 or H4 (obviously a positive number).

However, the database has reported the data based on enrichment scores (H3K14ac vs H3 for exmample) and negative numbers also exist among the data. I am having difficulty interpreting these negative results, especially that for some modifications (for example H3K9ac vs H3), one group of genes (the one that allegedly should be more active) has negative mean; while the other group ( supposedly less active) has a positive mean. 

Is anyone aware of the meaning of these numbers in this context? I thank you in advance

PS: Here is a link to access the database: http://cosbi3.ee.ncku.edu.tw/yna/main

chip-seq epigenetics genome • 595 views
ADD COMMENTlink modified 2.4 years ago by dyollluap300 • written 2.4 years ago by parsiabasimfar0
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gravatar for dyollluap
2.4 years ago by
dyollluap300
USA, California, Bay Area
dyollluap300 wrote:

The friendly folks at the SGD will probably have a strong (and very conservative) opinion about YNA... they do a manual curation process and are very familiar with some of the intricate details of the underlying studies. The SGD helpdesk is fairly active and they usually provide careful and complete responses to this kind of yeast community question.

ADD COMMENTlink written 2.4 years ago by dyollluap300

Thanks for the lead. I'm going to address this question to their staff.

ADD REPLYlink written 2.4 years ago by parsiabasimfar0
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