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Table S1 All of the proteins found in the study.

Table S2 The significant terms that were found to group when analysing the entire data set (N = 10).

Table S3 Melanosome and epidermal growth associated genes.

Table S4 The proteins that were only detected in one phenotype.

Table S5 The results for the ClueGO analysis when only using protein products identified in the black samples (= 5).

Table S6 The results for the ClueGO analysis when only using protein products identified in the brown samples (= 5). associated with a GO Term is given in the ‘% associated genes’ column.

Table S7 Results of the ClueGO analysis comparing brown samples and black samples.

Table S8 The 17 networks that were identified in the developing pied flycatcher feather proteome with the Ingenuity Pathway Analysis program.

Table S9 The effect sizes, 95% confidence intervals, confidence intervals for the bootstraps and bias C.I.s from the network expression analysis.

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