Abstract
This chapter is intended to introduce the fundamental principles of the heat map, the most widely used medium to present high-throughput data, to scientists unaccustomed to analyzing large data sets. Its scope includes describing the general features of heat maps, how their components are designed, the meaning of parameters such as “distance method” and “linkage method,” and the influence of manipulations such as row-scaling and logarithmic transformations on data interpretation and presentation. This chapter may serve as a guide to understanding the use of heat maps in published analyses or to aid in their design, allowing efficient interpretations of high-throughput experiments, exploration of hypotheses, or clear communications of findings.
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Notes
- 1.
In the pictured example (Fig. 1), the gradient scale spans −2 to 2 and represents log2 transformed normalized values. Normalization is to a representation of the average value (commonly employed in proteomics, but not discussed here). Thus 1 on the scale represents about twice the average value and −1 represents about half of the average value.
References
Zhu Y, Orre LM, Johansson HJ, Huss M, Boekel J, Vesterlund M, Fernandez-Woodbridge A, Branca RMM, Lehtio J (2018) Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. Nat Commun 9(1):903. https://doi.org/10.1038/s41467-018-03311-y
Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtio J (2017) Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome. Sci Rep 7(1):4513. https://doi.org/10.1038/s41598-017-04798-z
Ward JH (1963) Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58(301):236–244. https://doi.org/10.1080/01621459.1963.10500845
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Vacanti, N.M. (2019). The Fundamentals of Constructing and Interpreting Heat Maps. In: Fendt, SM., Lunt, S. (eds) Metabolic Signaling. Methods in Molecular Biology, vol 1862. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8769-6_20
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DOI: https://doi.org/10.1007/978-1-4939-8769-6_20
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