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. 2015 Jan 23;16(1):22. doi: 10.1186/s12864-014-1202-9

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© Chang et al.; licensee Biomed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Cosine similarity analysis methodology for determining co-differentially regulated genes in the feather/scale region. A) 2D representation of the concept of cosine similarity analysis. The actual analysis occurs in a 20-dimension hyperspace. θ represents the angles between a probe vector and a differentially expressed vector. B) 2D representation of the clustering concept after the identification of similarly regulated vectors. Differentially expressed genes and their correlated probes are represented by blue squares and green circles, respectively. The correlated differentially expressed genes and probes are clustered (encircled gene sets by the outlines of different colors representing different clusters). Some differentially expressed genes and probes may be clustered into more than one group. C) Demonstration of cosine value distribution for each seed. The cosine value distributions are normalized by Fisher transformation. The upper 0.5% and lower 0.5% mark the selection boundaries in choosing probes with similar regulation patterns. D) Distribution of genes that share common seeds. Genes sharing more than 10 common seeds are shortlisted for their potential roles in developmentally important pathways.