Fold change

Fold change is a measure describing how much a quantity changes going from an initial to a final value. For example, an initial value of 30 and a final value of 60 corresponds to a fold change of 1 (or equivalently, a change to 2 times), or in common terms, a one-fold increase. Fold change is calculated simply as the ratio of the difference between final value and the initial value over the original value. Thus, if the initial value is A and final value is B, the fold change is (B - A)/A or equivalently B/A - 1. As another example, a change from 80 to 20 would be a fold change of -0.75, while a change from 20 to 80 would be a fold change of 3 (a change of 3 to 4 times the original).

However, confusion and ambiguity can arise from this use. For example, although 1 fold is 100%, or 1x, a 1-fold increase, is, as noted above, understood by some to mean an increase of 200%, or a doubling, as in "60 is 2 times greater than 30." Yet, several dictionaries, including the Oxford English Dictionary[1] and Merriam-Webster Dictionary,[2] as well as Collins's Dictionary of Mathematics, define "-fold" to mean "times," as in "2-fold" = "2 times" = "double." Likely because of this definition, many scientists use not only fold but also fold change to be synonymous with "times," as in "3-fold larger" = "3 times larger."[3][4][5] Yet, among some experts in the field use persists of fold change as in "60 is 1-fold greater than 30." Therefore, one could argue that the use of fold change, as in "A is 2-fold greater than 30" should be avoided altogether, since some will interpret this to mean A is 60 whereas others will understand this to mean that A is 90.

Even more ambiguous is fold decrease, which is more precisely expressed as fractions.

Fold change is often used in analysis of gene expression data in microarray and RNA-Seq experiments, for measuring change in the expression level of a gene.[6] A disadvantage to and serious risk of using fold change in this setting is that it is biased [7] and may miss differentially expressed genes with large differences (B-A) but small ratios (A/B), leading to a high miss rate at high intensities.

Converting a fold change to a percentage change

As with any conversion to percent, multiply the fold change by 100.

See also

Notes

  1. ↑ http://public.oed.com/about/free-oed/
  2. ↑ http://www.merriam-webster.com/dictionary/twofold
  3. ↑ Cieńska M, Labus K, Lewańczuk M, Koźlecki T, Liesiene J, Bryjak J. (2016). "Effective L-Tyrosine Hydroxylation by Native and Immobilized Tyrosinase." PLOS One. 11: e0164213. doi:10.1371/journal.pone.0164213. PMID 27711193.
  4. ↑ Cunningham MW Jr, Williams JM, Amaral L, Usry N, Wallukat G, Dechend R, LaMarca B. (2016). "Agonistic Autoantibodies to the Angiotensin II Type 1 Receptor Enhance Angiotensin II–Induced Renal Vascular Sensitivity and Reduce Renal Function During Pregnancy." Hypertension. doi:10.1161/HYPERTENSIONAHA.116.07971. PMID 27698062.
  5. ↑ Li B, Li YY, Wu HM, Zhang FF, Li CJ, Li XX, Lambers H, Li L. (2015) "Root exudates drive interspecific facilitation by enhancing nodulation and N2 fixation." 113(23):6496-501. doi:10.1073/pnas.1523580113. PMID 27217575. PMCID: PMC4988560.
  6. ↑ Tusher, Virginia Goss; Tibshirani, Robert; Chu, Gilbert (2001). "Significance analysis of microarrays applied to the ionizing radiation response". Proceedings of the National Academy of Sciences of the United States of America. 98 (18): 5116–5121. doi:10.1073/pnas.091062498. PMC 33173Freely accessible. PMID 11309499.
  7. ↑ Mariani, TJ; Budhraja V; Mecham BH; Gu CC; Watson MA; Sadovsky Y. (2003). "A variable fold change threshold determines significance for expression microarrays". FASEB J. 17 (2): 321–323. doi:10.1096/fj.02-0351fje. PMID 12475896.

External links

This article is issued from Wikipedia - version of the 11/26/2016. The text is available under the Creative Commons Attribution/Share Alike but additional terms may apply for the media files.