pathways abundances

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cecilia silvestri

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Dec 1, 2019, 9:35:15 AM12/1/19
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I'm having trouble in understanding in which unit the pathways abundances are measured and if it is normal to have such a big variance in some pathways (e.g. from tenths in some subjects to thousands in other subjects). Thanks in advance.

Eric Franzosa

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Dec 2, 2019, 2:45:55 PM12/2/19
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Pathway abundance is measured in the same units as gene abundance: i.e. reads per kilobase (RPK), which is itself a measure of sequencing coverage depth. In the case of pathways, you can think of the measurement as being the coverage of the least-abundant reaction in the pathway or (speaking relative to other pathways in the same sample) the number of complete copies of the pathway in a sample.

Thanks,
Eric



On Sun, Dec 1, 2019 at 9:35 AM cecilia silvestri <ceciliasi...@gmail.com> wrote:
I'm having trouble in understanding in which unit the pathways abundances are measured and if it is normal to have such a big variance in some pathways (e.g. from tenths in some subjects to thousands in other subjects). Thanks in advance.

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cecilia silvestri

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Dec 5, 2019, 6:07:31 AM12/5/19
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Thank you very much! 
I have one last question, is there a dataset or a way to link a pathway to the bacteria species involved in it? 


Il giorno lunedì 2 dicembre 2019 20:45:55 UTC+1, Eric Franzosa ha scritto:
Pathway abundance is measured in the same units as gene abundance: i.e. reads per kilobase (RPK), which is itself a measure of sequencing coverage depth. In the case of pathways, you can think of the measurement as being the coverage of the least-abundant reaction in the pathway or (speaking relative to other pathways in the same sample) the number of complete copies of the pathway in a sample.

Thanks,
Eric



On Sun, Dec 1, 2019 at 9:35 AM cecilia silvestri <ceciliasi...@gmail.com> wrote:
I'm having trouble in understanding in which unit the pathways abundances are measured and if it is normal to have such a big variance in some pathways (e.g. from tenths in some subjects to thousands in other subjects). Thanks in advance.

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Eric Franzosa

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Dec 11, 2019, 3:58:20 PM12/11/19
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You can look up individual pathways in MetaCyc's own database, which includes information about the taxonomic distribution of different pathways.

Thanks,
Eric



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