Download Supplementary Figure S1. Numerical uncoupling between

Supplementary Figure S1. Numerical uncoupling between transcriptome and translatome
associated functional over represented terms. Terms enriched only in transcriptome DEGs are
displayed in cyan, terms enriched only in translatome DEGs are displayed in yellow, terms enriched
in both transcriptome and translatome DEGs are displayed in green.
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Supplementary Figure S2. Fraction of genes detected as DEGs (y axis) at different RankProd pfp
threshlolds (x axis). One graphic is displayed for each dataset. The last graphic shows the behavior
of all the datasets together. Uncoupling and coupling classes of DEGs are color labeled: genes with
significant variations only in the transcriptome (in cyan), genes with significant variations only in
the translatome (in yellow), genes with opposite significant variations between transcriptome and
translatome (in red), genes with homodirectional significant variations (in green).
2
Supplementary Figure S3. Independence between the fraction of detected DEGs and the average
Spearman correlation among replicas. For each transcriptome - translatome dataset of the collection,
the average correlation among replicas is plotted on the x axis, while the fraction of genes detected
as DEGs is plotted on the y axis.
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Supplementary Figure S4. Observed coupling frequencies are higher than what expected by
chance. All human, rat and mouse genes were divided in eight classes according to the number n1 of
their occurrences as DEGs across all the collected datasets (n1 ranging from a minimum of 1 to a
maximum of 8). For each gene, the number of occurrences as coupled was next counted. The
resulting distribution probabilities of coupling events are displayed in dark green. Expected
probabilities were calculated as multinomial distributions with n1 numbers of trials and coupling
probability = 0.35 (the average percentage of coupled DEGs observed across all the datasets). The
observed distributions are always higher than the expected distributions, suggesting the presence of
gene specific mechanisms that couple transcriptional and translational variations in a broad set of
conditions.
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Supplementary Figure S5. Uncoupling between significantly enriched IPA canonical pathways.
For each dataset, the number of pathways significantly enriched only for transcriptome DEGs (in
cyan), the number of pathways significantly enriched only for translatome DEGs (in yellow) and the
number of pathways enriched for both transcriptome and translatome DEGs (in green) are
displayed. Three datasets have no significantly enriched pathways. In 14 out of the 16 remaining
datasets, the number of specific pathways exceeds the number of common pathways.
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Gene Symbol
GPM6A
PSAPL1
AGR2
EGR1
PCIF1
EGR2
ZNF655
RPL27
SLC2A3
RPL10A
ACTB
GAPDH
HPRT1
TBP
Assay ID
Transcriptome log2 FC Translatome log2 FC
0.70
0.10
0.14
3.94
0.01
3.30
0.23
-0.18
0.64
0.03
-0.17
-0.02
0.06
0.11
Hs01009142_m1
Hs00999475_s1
Hs00180702_m1
Hs00152928_m1
Hs00363733_m1
Hs00166165_m1
Hs01002760_m1
Hs03044962_g1
Hs00359840_m1
Hs03043870_g1
Hs99999903_m1
Hs02758991_g1
Hs01003267_m1
Hs00427620_m1
1.28
2.06
-0.08
7.93
-0.22
6.98
0.09
0.13
0.77
-0.32
0.38
-0.17
-0.11
-0.15
Supplementary Table S1. TaqMan® Gene Expression Assays (Applied Biosystems) and results.
# probesets
on chip
# unambiguous
probesets
% of
mapping
loss
# ENSEMBL
genes
# avg
probesets for
gene
HG-U133_Plus_2
HG-U133A_2
HG_U95Av2
HG-U133A
Mouse
54675
22277
12625
22283
36666
19726
11399
19730
33%
11%
10%
11%
16440
11570
8100
11550
2.23
1.70
1.41
1.71
MG_U74Av2
Mouse430_2
MOE430A
Rat
12488
45101
22690
11174
33900
21186
11%
25%
7%
8250
16800
12390
1.35
2.02
1.71
Rat230_2
31099
18314
41%
12010
1.52
Affymetrix
Platform ID
Human
Supplementary Table S2. Differences among Affymetrix chips during the preprocessing stage of
data analysis. The table shows the number of probesets on the chip, the number of unambiguous
probesets, the percentage of probesets lost after the mapping step, the number of mapped
ENSEMBL genes and the average number of probesets mapping to a gene.
6
Cellular function
Metabolic Disease
Neurological Disease
Cellular Compromise
Free Radical Scavenging
RNA Post-Transcriptional Modification
Developmental Disorder
Skeletal and Muscular Disorders
Genetic Disorder
Gene Expression
Endocrine System Development and
Function
Drug Metabolism
Energy Production
Cell Death
Cardiovascular Disease
Glutathione Depletion In Liver
Cell-To-Cell Signaling and Interaction
Cell Morphology
Tissue Development
Cellular Development
Cellular Growth and Proliferation
Cellular Assembly and Organization
Cell Cycle
Cell Signaling
Connective Tissue Development and
Function
Antimicrobial Response
Organismal Injury and Abnormalities
Nervous System Development and Function
Organ Development
Connective Tissue Disorders
Reproductive System Development and
Function
RNA Trafficking
Hematological System Development and
Function
Inflammatory Response
Infectious Disease
Lipid Metabolism
Protein Synthesis
Skeletal and Muscular System Development
and Function
Nucleic Acid Metabolism
Amino Acid Metabolism
Number of
transcriptome
networks
Number of
translatome
networks
Translatome
network
specificity
1
3
2
2
4
5
2
17
37
6
11
6
6
9
11
4
25
53
0.71
0.57
0.50
0.50
0.38
0.38
0.33
0.19
0.18
5
9
6
52
4
5
41
12
26
39
37
52
49
15
7
12
8
66
5
6
48
14
30
43
40
56
49
15
0.17
0.14
0.14
0.12
0.11
0.09
0.08
0.08
0.07
0.05
0.04
0.04
0.00
0.00
13
7
7
6
5
4
13
7
7
6
5
4
0.00
0.00
0.00
0.00
0.00
0.00
4
3
4
3
0.00
0.00
36
28
12
48
16
35
26
11
43
14
-0.01
-0.04
-0.04
-0.05
-0.07
8
8
7
7
7
6
-0.07
-0.07
-0.08
7
Cancer
Cellular Movement
Immune Cell Trafficking
Endocrine System Disorders
Protein Degradation
Embryonic Development
Protein Folding
Small Molecule Biochemistry
DNA Replication
Immunological Disease
Molecular Transport
Cellular Function and Maintenance
Tissue Morphology
Carbohydrate Metabolism
and Repair
Reproductive System Disease
Recombination
Post-Translational Modification
Gastrointestinal Disease
Hematopoiesis
Hematological Disease
Inflammatory Disease
Dermatological Diseases and Conditions
Cardiovascular System Development and
Function
Antigen Presentation
Vitamin and Mineral Metabolism
Organismal Development
40
48
12
6
6
22
5
65
42
4
45
40
10
16
16
6
30
21
13
5
11
6
9
34
40
10
5
5
18
4
50
32
3
33
28
7
11
11
4
19
13
8
3
6
3
4
-0.08
-0.09
-0.09
-0.09
-0.09
-0.10
-0.11
-0.13
-0.14
-0.14
-0.15
-0.18
-0.18
-0.19
-0.19
-0.20
-0.22
-0.24
-0.24
-0.25
-0.29
-0.33
-0.38
14
7
7
13
6
3
2
3
-0.40
-0.40
-0.56
-0.63
Supplementary Table S3. Cellular functions associated to IPA networks across all the datasets.
Each significant network built by IPA from transcriptome or translatome DEGs is associated to
three cellular functions, based on the functional annotation of the nodes of the network. For each
cellular function, the number of associated transcriptome networks and the number of associated
translatome networks across all the datasets was calculated. For each function, a translatome
network specificity degree was calculated as the number of associated translatome networks minus
the number of associated transcriptome networks, divided by the total number of associated
networks. Only cellular functions with more than five associated networks were considered. In the
table, cellular functions are ordered from the most translatome specific to the most transcriptome
specific.
8