0.75

0.50

0.25

0.00

-0.25

-0.50

S f

acto

r

body

wei

ght d

urin

g W

M

body

wei

ght d

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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.

Factor Mean F ratio

3-way ANOVA

3-way ANCOVA

Class (successful,

unsuccessful)

5.78 2.28

Diet 2.36 1.00

Total Energy Intake

1.34

Individu 1.32 1.00

class diet energy subject error0

1

2

3

4

5

6

7

3-way ANOVA3-way ANCOVA

Factors

Mea

n F

rat

io

Supplementary figure 2: Exploratory analysesData 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

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.

ID Score Focus Molecules Top Functions

1 33 32Nervous System Development and Function, Carbohydrate Metabolism, Cell Death

2 31 31RNA Post-Transcriptional Modification, Gene Expression, Cell-To-Cell Signaling and Interaction

3 22 26Cellular Growth and Proliferation, Skeletal and Muscular System Development and Function, Gene Expression

4 12 17Cell-To-Cell Signaling and Interaction, Hematological System Development and Function, Infection Mechanism

5 11 18 Cellular Growth and Proliferation, Gene Expression, Cancer

6 10 17 Cell Death, Cancer, Cellular Growth and Proliferation

7 9 15 Cell Death, Respiratory Disease, Cancer

8 9 16 Protein Synthesis, Gene Expression, Infectious Disease

9 9 16Gene Expression, Reproductive System Development and Function, Infection Mechanism

10 8 15Cellular Assembly and Organization, Cellular Compromise, Gene Expression

11 8 14 Cell Cycle, Cancer, Cellular Development12 7 14 Cancer, Tumor Morphology, Cell Cycle

13 7 10Tissue Development, Cell Signaling, Post-Translational Modification

14 7 14Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking

15 7 14 Cell Cycle, Cellular Growth and Proliferation, Cancer

16 7 14 Cancer, Organ Development, Tumor Morphology

17 7 14 Cell Signaling, Gene Expression, Cell Death

18 7 14Cell Cycle, Cellular Growth and Proliferation, Connective Tissue Development and Function

19 6 13 Cell Cycle, Cancer, Cellular Growth and Proliferation

Supplementary figure 4: Networks associated with genes differentiating successful and unsuccessful groups as annotated by Ingenuity Pathways Analysis.