Table S1. Pathway analysis of up-regulated proteins in MV4-11 cells treated with MLN4924
Pathway identifier
Pathway name
# Entities
found
# Entities
total
Entities ratio
Entities PValue
REACT_1783
G1/S Transition
G2/M DNA
replication
checkpoint
Mitotic G1-G1/S
phases
S Phase
Detoxification of
Reactive Oxygen
Species
G2/M Checkpoints
Association of
licensing factors with
the pre-replicative
complex
Cell Cycle
DNA Replication
Synthesis and
interconversion of
nucleotide di- and
triphosphates
G1/S-Specific
Transcription
Cell Cycle, Mitotic
Cell Cycle
Checkpoints
5
113
0.01130226
3.37E-04
2
7
7.00E-04
6.60E-04
5
5
139
139
0.013902781
0.013902781
8.56E-04
8.56E-04
3
3
52
53
0.00520104
0.00530106
0.002714252
0.002863216
2
9
4
15
579
117
0.0015003
0.057911582
0.01170234
0.002947885
0.00318196
0.003479343
3
57
0.00570114
0.003509128
2
8
17
496
0.00170034
0.049609922
0.003760874
0.00440028
4
128
0.012802561
0.004776118
REACT_1846
REACT_21267
REACT_899
REACT_264249
REACT_828
REACT_1181
REACT_115566
REACT_383
REACT_21330
REACT_683
REACT_152
REACT_1538
REACT_1574
REACT_1006
REACT_207
REACT_829
REACT_1857
REACT_471
REACT_120956
REACT_2014
REACT_264071
REACT_264075
REACT_2198
REACT_1698
REACT_405
REACT_2174
Cyclin E associated
events during G1/S
transition
Polo-like kinase
mediated events
Removal of licensing
factors from origins
Regulation of DNA
replication
Cyclin A/B1
associated events
during G2/M
transition
E2F mediated
regulation of DNA
replication
Cellular responses to
stress
Synthesis of DNA
HSF1 activation
Attenuation phase
Translesion
synthesis by Y family
DNA polymerases
bypasses lesions on
DNA template
Metabolism of
nucleotides
Transport of the
SLBP Dependant
Mature mRNA
DNA Damage
Bypass
3
69
0.00690138
0.005953821
2
23
0.00230046
0.006746026
3
74
0.00740148
0.007209485
3
77
0.00770154
0.008032697
2
26
0.00260052
0.008533888
2
33
0.00330066
0.013427605
6
3
2
2
374
108
43
46
0.037407481
0.01080216
0.00430086
0.00460092
0.013971662
0.019770763
0.022046501
0.024978056
2
46
0.00460092
0.024978056
4
216
0.021604321
0.027588729
1
6
6.00E-04
0.031315108
2
55
0.0055011
0.034651218
REACT_264164
REACT_1949
REACT_2122
REACT_338
REACT_2243
REACT_13594
REACT_13639
REACT_268571
REACT_9029
REACT_1156
REACT_2148
REACT_1364
HSF1-dependent
transactivation
CDT1 association
with the
CDC6:ORC:origin
complex
ChREBP activates
metabolic gene
expression
Transport of Mature
mRNAs Derived from
Intronless Transcripts
Assembly of the prereplicative complex
Neurotransmitter
uptake and
Metabolism In Glial
Cells
Astrocytic GlutamateGlutamine Uptake
And Metabolism
Uptake and function
of diphtheria toxin
Cyclin A:Cdk2associated events at
S phase entry
Orc1 removal from
chromatin
Switching of origins
to a post-replicative
state
SLBP Dependent
Processing of
2
56
0.00560112
0.035803209
2
58
0.00580116
0.038151276
1
8
8.00E-04
0.041538091
1
9
9.00E-04
0.046609813
2
67
0.00670134
0.049409734
1
10
0.0010002
0.051655201
1
10
0.0010002
0.051655201
1
10
0.0010002
0.051655201
2
70
0.0070014
0.053399718
2
72
0.00720144
0.05612168
2
72
0.00720144
0.05612168
1
11
0.00110022
0.056674389
REACT_150266
REACT_111174
REACT_407
REACT_734
REACT_1725
REACT_7999
REACT_12564
REACT_70
REACT_897
REACT_355141
REACT_1385
REACT_355303
ReplicationDependent Histone
Pre-mRNAs
Establishment of
Sister Chromatid
Cohesion
Cross-presentation of
particulate
exogenous antigens
(phagosomes)
Chk1/Chk2(Cds1)
mediated inactivation
of Cyclin B:Cdk1
complex
DNA Replication PreInitiation
M/G1 Transition
Removal of the Flap
Intermediate from the
C-strand
AKT phosphorylates
targets in the cytosol
Removal of the Flap
Intermediate
G2/M DNA damage
checkpoint
RHO GTPases
Activate NADPH
Oxidases
Processive synthesis
on the lagging strand
RHO GTPases
activate CIT
1
13
0.00130026
0.066634702
1
13
0.00130026
0.066634702
1
14
0.00140028
0.071576091
2
2
85
85
0.0085017
0.0085017
0.074930155
0.074930155
1
15
0.0015003
0.076491811
1
15
0.0015003
0.076491811
1
18
0.00180036
0.091086257
1
18
0.00180036
0.091086257
1
19
0.00190038
0.0959006
1
20
0.0020004
0.100689921
1
20
0.0020004
0.100689921
REACT_22297
REACT_355377
REACT_355048
REACT_8027
REACT_1768
REACT_264245
REACT_1287
REACT_1439
REACT_264165
REACT_264155
REACT_21352
REACT_312
REACT_571
REACT_125
Heme degradation
TP53 Regulates
Metabolic Genes
Transcriptional
Regulation by TP53
Processive synthesis
on the C-strand of
the telomere
Processing of
Capped Intronless
Pre-mRNA
HATs acetylate
histones
Translesion
Synthesis by POLH
Common Pathway of
Fibrin Clot Formation
Chromatin modifying
enzymes
Chromatin
organization
RNA Polymerase I/
Mitochondrial
Transcription
Lagging Strand
Synthesis
RNA Polymerase III
Transcription
Initiation From Type
3 Promoter
Processing of
Capped IntronContaining Pre-
1
20
0.0020004
0.100689921
2
103
0.01030206
0.103713113
2
103
0.01030206
0.103713113
1
21
0.00210042
0.105454347
1
23
0.00230046
0.114909024
2
110
0.0110022
0.115615609
1
24
0.00240048
0.119599526
1
25
0.0025005
0.124265638
3
233
0.023304661
0.126197083
3
233
0.023304661
0.126197083
2
120
0.0120024
0.133186525
1
27
0.00270054
0.133525186
1
28
0.00280056
0.13811887
2
125
0.012502501
0.14219138
REACT_1281
REACT_655
REACT_120919
REACT_263897
REACT_11052
REACT_11066
REACT_355468
REACT_2203
REACT_21391
REACT_1095
REACT_355250
REACT_264464
REACT_281
REACT_7961
REACT_12529
REACT_932
mRNA
Transport of Mature
Transcript to
Cytoplasm
Pyrimidine salvage
reactions
Synthesis of PE
Cellular response to
heat stress
Metabolism of noncoding RNA
snRNP Assembly
Constitutive
Signaling by AKT1
E17K in Cancer
G2/M Transition
Mitotic G2-G2/M
phases
Activation of the prereplicative complex
Termination of
translesion DNA
synthesis
VEGFA-VEGFR2
Pathway
RNA Polymerase III
Transcription
Initiation
Telomere C-strand
(Lagging Strand)
Synthesis
Signaling by VEGF
DNA strand
1
29
0.00290058
0.142688657
1
1
30
30
0.0030006
0.0030006
0.14723467
0.14723467
2
128
0.012802561
0.147656839
1
1
31
31
0.00310062
0.00310062
0.151757029
0.151757029
1
2
31
133
0.00310062
0.013302661
0.151757029
0.156861411
2
135
0.013502701
0.160574373
1
33
0.00330066
0.160731269
1
33
0.00330066
0.160731269
2
137
0.013702741
0.164303983
1
35
0.0035007
0.169612336
1
2
1
35
146
38
0.0035007
0.014602921
0.00380076
0.169612336
0.181273616
0.182761311
REACT_107
REACT_6769
REACT_1590
REACT_821
REACT_1371
REACT_22339
REACT_2051
REACT_8030
REACT_355474
REACT_387
REACT_894
REACT_6960
REACT_116145
REACT_953
elongation
Apoptotic cleavage of
cellular proteins
Activation of ATR in
response to
replication stress
G1 Phase
Cyclin D associated
events in G1
RNA Polymerase III
Transcription
RNA Polymerase III
Abortive And
Retractive Initiation
Formation of Fibrin
Clot (Clotting
Cascade)
Extension of
Telomeres
RHO GTPase
Effectors
Cleavage of Growing
Transcript in the
Termination Region
RNA Polymerase II
Transcription
Termination
Glutathione synthesis
and recycling
PPARA activates
gene expression
RNA Polymerase I
Transcription
1
38
0.00380076
0.182761311
1
1
39
42
0.00390078
0.00420084
0.187098738
0.19997595
1
42
0.00420084
0.19997595
1
42
0.00420084
0.19997595
1
42
0.00420084
0.19997595
1
42
0.00420084
0.19997595
1
42
0.00420084
0.19997595
3
293
0.029305861
0.202891509
1
43
0.00430086
0.204223714
1
43
0.00430086
0.204223714
1
43
0.00430086
0.204223714
2
169
0.016903381
0.225674211
1
49
0.00490098
0.229249495
REACT_238
REACT_19241
REACT_13565
REACT_9431
REACT_216
REACT_25325
REACT_995
REACT_264041
REACT_9003
REACT_85
REACT_1625
REACT_121256
Initiation
Amino acid synthesis
and interconversion
(transamination)
Regulation of lipid
metabolism by
Peroxisome
proliferator-activated
receptor alpha
(PPARalpha)
Regulation of
ornithine
decarboxylase
(ODC)
Metabolism of
porphyrins
DNA Repair
AUF1 (hnRNP D0)
destabilizes mRNA
Apoptotic execution
phase
Uptake and actions
of bacterial toxins
SCF(Skp2)-mediated
degradation of
p27/p21
p53-Dependent G1/S
DNA damage
checkpoint
p53-Dependent G1
DNA Damage
Response
Phagosomal
1
49
0.00490098
0.229249495
2
172
0.017203441
0.231539899
1
51
0.00510102
0.237418557
1
2
54
183
0.00540108
0.018303661
0.249513109
0.253128156
1
55
0.0055011
0.253502649
1
55
0.0055011
0.253502649
1
56
0.00560112
0.257471379
1
58
0.00580116
0.265346833
1
60
0.0060012
0.273140318
1
1
60
60
0.0060012
0.0060012
0.273140318
0.273140318
REACT_25060
REACT_263923
REACT_169185
REACT_2254
REACT_75820
REACT_7970
REACT_6926
REACT_1974
REACT_957
REACT_75842
REACT_13
REACT_1309
REACT_115639
maturation (early
endosomal stage)
Iron uptake and
transport
HDACs deacetylate
histones
DNA
Damage/Telomere
Stress Induced
Senescence
G1/S DNA Damage
Checkpoints
Class I MHC
mediated antigen
processing &
presentation
Telomere
Maintenance
Glutathione
conjugation
RNA Polymerase I
Promoter Clearance
Pyrimidine
metabolism
Antigen processing:
Ubiquitination &
Proteasome
degradation
Metabolism of amino
acids and derivatives
RNA Polymerase I
Transcription
Sulfur amino acid
1
61
0.00610122
0.277006584
1
63
0.00630126
0.284678681
1
63
0.00630126
0.284678681
1
63
0.00630126
0.284678681
3
357
0.035707141
0.29368562
1
73
0.00730146
0.321856974
1
74
0.00740148
0.325468821
1
80
0.0080016
0.346746882
1
81
0.00810162
0.350228613
2
235
0.023504701
0.354880769
3
399
0.039907982
0.355054175
1
1
83
84
0.00830166
0.00840168
0.357137542
0.360564926
REACT_169168
REACT_11044
REACT_318
REACT_24994
REACT_1280
REACT_22172
REACT_264487
REACT_121237
REACT_1366
REACT_147723
REACT_467
REACT_1735
REACT_75829
metabolism
SenescenceAssociated Secretory
Phenotype (SASP)
Signaling by Rho
GTPases
Platelet
degranulation
Regulation of mRNA
stability by proteins
that bind AU-rich
elements
Response to
elevated platelet
cytosolic Ca2+
Chromosome
Maintenance
Regulation of HSF1mediated heat shock
response
Latent infection of
Homo sapiens with
Mycobacterium
tuberculosis
RNA Polymerase II
Transcription
PI3K/AKT Signaling
in Cancer
mRNA Splicing Major Pathway
mRNA Splicing
PIP3 activates AKT
signaling
1
85
0.0085017
0.363974381
3
406
0.040608122
0.365273502
1
88
0.00880176
0.374096083
1
90
0.0090018
0.380755909
1
95
0.0095019
0.397102794
1
101
0.01010202
0.41616086
1
108
0.01080216
0.437649046
1
109
0.01090218
0.440654746
1
110
0.0110022
0.443644684
1
115
0.0115023
0.45836074
1
1
119
119
0.01190238
0.01190238
0.469858003
0.469858003
1
120
0.0120024
0.472694697
REACT_115961
REACT_355304
REACT_355450
REACT_355160
REACT_355552
REACT_116008
REACT_12464
REACT_12578
REACT_71
REACT_355252
REACT_1505
REACT_22279
REACT_24970
REACT_121401
REACT_111040
REACT_578
REACT_111119
PI3K events in
ERBB4 signaling
PI-3K
cascade:FGFR4
PI-3K
cascade:FGFR2
PI-3K
cascade:FGFR3
PI-3K
cascade:FGFR1
PI3K events in
ERBB2 signaling
PI3K/AKT activation
GAB1 signalosome
Gene Expression
RHO GTPases
Activate Formins
Integration of energy
metabolism
Fatty acid,
triacylglycerol, and
ketone body
metabolism
Factors involved in
megakaryocyte
development and
platelet production
Glycerophospholipid
biosynthesis
Signaling by SCFKIT
Apoptosis
Antigen processing-
1
120
0.0120024
0.472694697
1
120
0.0120024
0.472694697
1
120
0.0120024
0.472694697
1
120
0.0120024
0.472694697
1
120
0.0120024
0.472694697
1
1
1
8
120
123
124
1423
0.0120024
0.01230246
0.01240248
0.142328466
0.472694697
0.481115725
0.483893303
0.487762431
1
135
0.013502701
0.51350012
1
139
0.013902781
0.523847672
2
335
0.033506701
0.533917615
1
150
0.015003001
0.551202842
1
157
0.015703141
0.567801488
1
1
1
168
171
176
0.016803361
0.017103421
0.017603521
0.592675599
0.599212053
0.609878163
REACT_268456
REACT_115596
REACT_252869
REACT_97307
REACT_355063
REACT_355265
REACT_169274
REACT_17025
REACT_118638
REACT_147814
REACT_115755
REACT_355408
REACT_252852
REACT_355289
REACT_355200
REACT_9470
REACT_9417
REACT_147694
REACT_120870
Cross presentation
Programmed Cell
Death
Signaling by ERBB4
Downstream
signaling of activated
FGFR4
Downstream
signaling of activated
FGFR3
Downstream
signaling of activated
FGFR1
Downstream
signaling of activated
FGFR2
Cellular Senescence
Downstream signal
transduction
Downstream
signaling events of B
Cell Receptor (BCR)
DAP12 signaling
Signaling by ERBB2
Signaling by FGFR4
Signaling by FGFR3
Signaling by FGFR1
Signaling by FGFR2
Signaling by FGFR
Signaling by EGFR
DAP12 interactions
Phospholipid
metabolism
1
1
179
180
0.017903581
0.018003601
0.61614362
0.618210084
1
182
0.018203641
0.622310321
1
182
0.018203641
0.622310321
1
182
0.018203641
0.622310321
1
1
182
183
0.018203641
0.018303661
0.622310321
0.624344207
1
193
0.019303861
0.644101075
1
1
1
1
1
1
1
1
1
1
195
196
196
196
196
197
199
200
212
213
0.019503901
0.019603921
0.019603921
0.019603921
0.019603921
0.019703941
0.019903981
0.020004001
0.021204241
0.021304261
0.647928296
0.649826735
0.649826735
0.649826735
0.649826735
0.651715129
0.655461992
0.657320564
0.678870512
0.680605104
1
215
0.021504301
0.684046756
REACT_16888
REACT_6959
REACT_12056
REACT_798
REACT_75774
REACT_13477
REACT_355497
REACT_163769
REACT_604
REACT_11061
REACT_13685
REACT_118773
REACT_355457
REACT_12627
REACT_163936
REACT_111217
REACT_13433
REACT_22258
REACT_116125
REACT_6900
Signaling by PDGF
Phase II conjugation
NGF signalling via
TRKA from the
plasma membrane
Platelet activation,
signaling and
aggregation
Adaptive Immune
System
Transmission across
Chemical Synapses
Infectious disease
Role of
LAT2/NTAL/LAB on
calcium mobilization
Hemostasis
Signalling by NGF
Neuronal System
Signaling by the B
Cell Receptor (BCR)
Diseases of signal
transduction
Generic Transcription
Pathway
Fc epsilon receptor
(FCERI) signaling
Metabolism
Biological oxidations
Metabolism of lipids
and lipoproteins
Disease
Immune System
1
1
224
234
0.022404481
0.023404681
0.699089238
0.714979675
1
241
0.024104821
0.725610084
1
248
0.024804961
0.735851217
4
928
0.092818564
0.736988418
1
2
259
524
0.025905181
0.052410482
0.751191409
0.773316765
1
2
1
1
284
561
327
338
0.028405681
0.056111222
0.032706541
0.033806761
0.782878297
0.805498383
0.828372334
0.838418483
1
357
0.035707141
0.854429165
1
360
0.036007201
0.856810608
2
633
0.063312663
0.856910546
1
11
1
368
2727
455
0.036807361
0.272754551
0.045509102
0.862975824
0.891486119
0.9152958
3
3
4
1107
1146
1601
0.110722144
0.114622925
0.160132026
0.942349953
0.951183852
0.978492444
REACT_15518
REACT_6802
REACT_111102
Transmembrane
transport of small
molecules
Innate Immune
System
Signal Transduction
1
787
0.078715743
0.987032285
1
4
924
2579
0.092418484
0.25795159
0.994139441
0.999841112