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af-lab / histone-catalogue

Core histone catalogue --- Live manuscript
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missing H1 on several values #22

Closed carandraug closed 8 years ago

carandraug commented 8 years ago

Throughout the text, we mention total number of histones genes and unique proteins. Such number does not include H1. Once upon a time, the text said something about referring to canonical core histones only when saying canonical histones for sake of brevity (or something around those lines). I can't find that text anymore.

Should we fix this by making it clear we talk about core histones only? Or change the code to include H1 too (as long it's just counting, this seems simple)?

Examples:

Canonical histones contribute the majority of proteins to the bulk structure and generic function of chromatin, and are encoded by 81 genes in 4 clusters in the human genome, of which 64 are coding genes and 17 are pseudogenes.

Again, this does not include H1 histones

The set of annotated human histone variant genes includes 32 members which are listed in Table S10 for completeness.

The table lists all variants, including H1, but the number 32, only includes core histones.

carandraug commented 8 years ago

We should cut down on mentioning H1 since part of our view is that H1 should not even an histone.

carandraug commented 8 years ago

I am done with my part here. I have removed dealing with H1 on the code, fixed the tex variables names, and already cleared up some confusion I found on the text manuscript.

Andrew, can you recheck the text for other instances of possible mix-ups ?

aflaus commented 8 years ago

To ensure the correct distinction between canonical histones (including H1) versus canonical core histones (excluding H1), a search for “canonical” was made and all instances were edited appropriately. Note that any use which includes H1 or specifies the histone type (e.g. “canonical H3”) does not need the specifier “core”. See commit 9429a8984fb09973cfeb635ed001f746758c724c