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So I wrote in a chapter that I will be checking for publications with gene lists in them. I got a comment asking "How would you define a gene list and what criteria did I use". I know that gene lists are usually generated by microarray studies, NGS analysis etc but what is the best way to define a gene list?

I am running blank except maybe say that its a list of genes.

EDIT: "I defined a gene list as a list of genes generated as a result of a microarray analysis or a next generation sequencing study." Sounds good?

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  • $\begingroup$ Correct me if I am wrong, but from your bio I suspect your background is in the numerate rather than the biological sciences. If so that would explain why your question "lacks context" (@Michael_A) or "is unclear" in SE Biology terms. A "gene list" means almost nothing, even with the rider "generated by microarray or NGS analysis". Just as a list of cars is almost meaningless, even if quaified by "generated by perusing newspapers". You must define the purpose of the experiments. Genes expressed in growing animal cells, after heat shock, after hormone treatment, in liver etc. $\endgroup$ – David Jul 23 '18 at 14:14
  • $\begingroup$ @David My work was to essentially get the number of publications with gene lists in them so as to make an argument that there are such a lot of lists being produced with potentially no follow up analysis being done on the majority of these lists generated in different studies. That is why I could not provide biological context to the question. Do not jump the gun, downvote and then vote to close before I get a chance to respond to your comment David. $\endgroup$ – The Last Word Jul 23 '18 at 14:37
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    $\begingroup$ The comment explained the down and close votes which were (and are) based solely on the question. I was not obliged to do this but felt it might be of use. $\endgroup$ – David Jul 23 '18 at 14:50
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    $\begingroup$ @David Of course you are not obliged, its just good practice. I hope I was able to explain the context of the question to your satisfaction. Have a good day. $\endgroup$ – The Last Word Jul 23 '18 at 14:54
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The comment seems useful as your current definition of a gene list lacks context.

How would you define a gene list?

There are many different kinds of gene list. Specifying gene lists from microarray and next-generation sequencing provides some context but both technologies are used to analyse many different kinds of DNA and RNA samples. Define the molecules that are being referenced by the gene lists.

Defining DNA or RNA isn't sufficient as each gene list is compiled to perform a research task. Genomic projects may provide lists of genes that were sequenced or mutated or contained single nucleotide polymorphisms. An RNA transcript project may create lists of genes where transcription was occurring in a tissue or whose RNA transcripts were influenced by experimental factors or whose splicing was altered. Most publications also include multiple gene lists and some of those will include rows that were removed following data evaluation. Define the kind of lists that you are collecting.

There's value in defining your search criteria well. It allows you to communicate your work to others and it can provide focus to your search efforts.

What criteria did I use?

This was mostly answered above. I would also consider including some rules for the publications that you will search for gene lists.

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