1. 0.75 0.50 0.25 0.00 -0.25 -0.50 S factor  body weight during WM  body weight during ER Supplementary figure 1: S factor distribution in each diet. S factor corresponds to weight variations during WM normalized by the weight loss during ER. Two populations were defined according to S factor, those subjects stabilizing or continuing to lose weight were classified as successful subjects (green circles), and those subjects regaining weight were classified as unsuccessful subjects (red circles). LGI: low glycemic index-; HGI: high glycemic index-; LP: low protein-; HP: high protein-diet.

2. FactorMean F ratio 3-way ANOVA 3-way ANCOVA Class (successful, unsuccessful) 5.782.28 Diet2.361.00 Total Energy Intake 1.34 Individu1.321.00 Supplementary figure 2: Exploratory analyses Data was validated by both multivariate principal component analysis (PCA) and univariate 3-way ANOVA. A: multivariate principal component analysis first two compontents [t1] and [t2] explained the 12.5% and the the 10.7%. of the total variance, respectively. triangle. LGI/LP diet; box. HGI/LP diet; dot. LGI/HP diet; diamond. HGI/HP diet; in black. successful group; in grey. unsuccessful group B: univariate 3-way ANOVA with (ANCOVA) energy intake as cofactor. Both analysis show that the main source of variation in gene expression dataset was the difference between successful and unsuccessful groups (class). A B

3. Supplementary figure 3: Hierarchical clustering of genes differentiating between successful and unsuccessful groups independently of diet composition. These transcripts were significant to both multivariate analysis and ANCOVA analysis (VIP > 1, qValue < 0.05, respectively). Su: successful group; Un: unsuccessful group; LGI: low glycemic index-; HGI: high glycemic index-; LP: low protein-; HP: high protein-diet.

4. IDScoreFocus MoleculesTop Functions 13332 Nervous System Development and Function, Carbohydrate Metabolism, Cell Death 231 RNA Post-Transcriptional Modification, Gene Expression, Cell-To-Cell Signaling and Interaction 32226 Cellular Growth and Proliferation, Skeletal and Muscular System Development and Function, Gene Expression 41217 Cell-To-Cell Signaling and Interaction, Hematological System Development and Function, Infection Mechanism 51118Cellular Growth and Proliferation, Gene Expression, Cancer 61017Cell Death, Cancer, Cellular Growth and Proliferation 7915Cell Death, Respiratory Disease, Cancer 8916Protein Synthesis, Gene Expression, Infectious Disease 9916 Gene Expression, Reproductive System Development and Function, Infection Mechanism 10815 Cellular Assembly and Organization, Cellular Compromise, Gene Expression 11814Cell Cycle, Cancer, Cellular Development 12714Cancer, Tumor Morphology, Cell Cycle 13710 Tissue Development, Cell Signaling, Post-Translational Modification 147 Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking 15714Cell Cycle, Cellular Growth and Proliferation, Cancer 16714Cancer, Organ Development, Tumor Morphology 17714Cell Signaling, Gene Expression, Cell Death 18714 Cell Cycle, Cellular Growth and Proliferation, Connective Tissue Development and Function 19613Cell Cycle, Cancer, Cellular Growth and Proliferation Supplementary figure 4: Networks associated with genes differentiating successful and unsuccessful groups as annotated by Ingenuity Pathways Analysis.