Download Table S1: Changes of functional categories on the proteome and

Table S1: Changes of functional categories on the proteome and genome level. Gene ontology (GO)
biological processes (GOBP), molecular functions (GOMF), cellular compartments (GOCC), KEGG
pathways, molecular complexes (Corum) and chromosomes were analyzed using two-dimensional
annotation analysis algorithm (see Methods). Significant changes were determined with a maximum false
discovery rate (FDR) of 0.05.
HCC2218
Cell
Type
Name
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Corum
Corum
Corum
GOBP
GOBP
GOBP
GOBP
5
3
2
1
X
4
16
20
13
8
14
18
7
11
22
12
17
55S ribosome, mitochondrial
39S ribosomal subunit, mitochondrial
Ribosome, cytoplasmic
cell communication
cell adhesion
signal transduction
biological adhesion
regulation of actin polymerization or
depolymerization
cell motion
translational elongation
mitochondrial part
mitochondrial inner membrane
organelle inner membrane
cytoskeleton
cytoplasm
mitochondrion
mitochondrial membrane
cytosol
mitochondrial matrix
integral to membrane
intrinsic to membrane
cytoskeletal part
organelle membrane
cell-substrate adherens junction
GOBP
GOBP
GOBP
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
Proteome
change
Genome
change
FDR
0.1
-0.2
-0.2
0.1
-0.1
-0.1
-0.1
0.1
-0.2
0.1
0.1
0.0
-0.1
0.0
0.1
-0.1
0.1
0.5
0.6
-0.4
-0.2
-0.4
-0.2
-0.4
0.5
-0.5
-0.7
0.3
-0.4
-0.4
-0.4
0.4
-0.6
0.3
0.3
-0.4
0.2
0.2
0.2
0.1
0.0
0.1
0.1
-0.1
0.0
0.1
0.0
0.1
0.0E+00
0.0E+00
0.0E+00
2.1E-13
4.4E-09
4.7E-09
1.9E-08
2.8E-07
5.6E-07
2.7E-06
1.5E-05
2.9E-05
8.5E-05
1.9E-03
1.2E-02
1.3E-02
2.1E-02
6.1E-04
3.6E-03
4.2E-03
3.7E-03
4.1E-03
5.3E-03
1.1E-02
-0.6
0.0
1.5E-02
-0.4
-0.4
0.4
0.5
0.5
-0.4
-0.2
0.3
0.4
-0.2
0.4
0.2
0.2
-0.3
0.1
-0.5
0.2
-0.1
0.0
-0.1
-0.1
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.1
2.2E-02
3.8E-02
0.0E+00
3.9E-08
4.3E-07
1.2E-06
3.0E-06
3.3E-06
5.5E-06
1.1E-05
6.2E-05
1.5E-04
3.6E-04
2.3E-03
1.2E-02
1.4E-02
HCC1143
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOMF
GOMF
GOMF
GOMF
KEGG
KEGG
KEGG
KEGG
KEGG
KEGG
KEGG
KEGG
KEGG
KEGG
KEGG
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Chromosome
Corum
Corum
Corum
Corum
Corum
Corum
Corum
GOBP
GOBP
GOBP
cytosolic part
cell-substrate junction
nucleoid
cell projection
adherens junction
mitochondrial nucleoid
membrane part
focal adhesion
cytoskeletal protein binding
actin binding
cation transmembrane transporter activity
ion transmembrane transporter activity
Oxidative phosphorylation
Regulation of actin cytoskeleton
Focal adhesion
Parkinson's disease
Ribosome
Huntington's disease
Alzheimer's disease
Leukocyte transendothelial migration
MAPK signaling pathway
Pathways in cancer
Cardiac muscle contraction
22
4
X
8
3
16
20
11
7
14
18
21
19
5
15
17
Spliceosome
ALL-1 supercomplex
C complex spliceosome
Respiratory chain complex I
(holoenzyme), mitochondrial
Ribosome, cytoplasmic
anti-HDAC2 complex
SNF2h-cohesin-NuRD complex
nucleobase, nucleoside, nucleotide and
nucleic acid metabolic process
transcription
nitrogen compound metabolic process
-0.4
-0.5
0.5
-0.3
-0.4
0.5
0.1
-0.5
-0.3
-0.4
0.4
0.4
0.5
-0.5
-0.5
0.4
-0.4
0.3
0.3
-0.4
-0.3
-0.3
0.5
0.3
-0.2
0.0
0.1
0.0
-0.1
0.2
-0.1
-0.1
0.1
0.1
0.3
0.2
-0.1
-0.1
0.0
0.4
0.7
0.4
-0.1
0.1
-0.1
0.0
0.0
-0.1
0.0
0.1
0.0
0.0
0.0
-0.1
0.0
0.0
0.0
0.0
0.0
0.0
0.0
-0.1
0.0
0.0
0.1
0.7
-0.5
-0.4
0.4
0.3
-0.3
0.3
-0.3
-0.2
0.3
0.4
0.4
0.1
-0.2
-0.2
0.1
0.1
-0.2
0.1
1.7E-02
1.7E-02
2.1E-02
2.1E-02
2.2E-02
3.6E-02
3.7E-02
3.7E-02
1.8E-04
2.7E-04
6.0E-03
6.7E-03
4.5E-05
4.9E-05
7.2E-05
1.3E-03
1.4E-03
7.9E-03
3.3E-02
3.5E-02
3.7E-02
3.9E-02
4.3E-02
0.0E+00
4.1E-14
2.3E-07
4.8E-07
5.5E-07
1.8E-06
2.4E-06
2.5E-06
7.9E-05
1.5E-04
1.7E-04
1.8E-04
4.5E-04
2.8E-03
1.9E-02
2.8E-02
4.6E-05
3.3E-03
1.0E-02
-0.7
-0.1
1.1E-02
-0.4
0.7
0.7
0.0
-0.2
-0.2
1.4E-02
2.5E-02
2.8E-02
0.2
0.0
0.0E+00
0.3
0.2
0.0
0.0
5.2E-08
6.7E-08
GOBP
GOBP
GOBP
GOBP
GOBP
GOBP
GOBP
GOBP
GOBP
GOBP
GOBP
GOBP
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOCC
GOMF
GOMF
GOMF
GOMF
GOMF
GOMF
GOMF
GOMF
GOMF
KEGG
KEGG
KEGG
chromatin organization
DNA metabolic process
regulation of transcription, DNAdependent
DNA replication
RNA splicing, via transesterification
reactions with bulged adenosine as
nucleophile
RNA splicing, via transesterification
reactions
nuclear mRNA splicing, via spliceosome
nuclear division
transport
mitochondrial electron transport, NADH
to ubiquinone
lipid metabolic process
mitosis
nuclear part
nucleus
chromosomal part
chromatin remodeling complex
nucleoplasm
spliceosomal complex
nucleoplasm part
mitochondrial respiratory chain complex I
NADH dehydrogenase complex
membrane
ribosome
chromatin
nuclear body
ribosomal subunit
nucleolus
DNA binding
nucleic acid binding
structural molecule activity
structural constituent of ribosome
NADH dehydrogenase activity
NADH dehydrogenase (ubiquinone)
activity
transcription factor activity
chromatin binding
oxidoreductase activity, acting on NADH
or NADPH
DNA replication
Ribosome
Focal adhesion
0.4
0.3
-0.1
0.0
3.0E-06
5.1E-06
0.2
0.0
3.2E-05
0.4
-0.1
1.4E-03
0.4
0.1
2.4E-03
0.4
0.1
2.6E-03
0.4
0.4
-0.1
0.1
0.0
0.0
2.9E-03
3.7E-03
8.0E-03
-0.7
-0.1
1.4E-02
-0.2
0.4
0.3
0.2
0.4
0.5
0.3
0.4
0.3
-0.7
-0.7
-0.1
-0.3
0.4
0.3
-0.3
0.2
0.3
0.2
-0.2
-0.3
-0.7
0.0
-0.1
0.0
0.0
-0.2
-0.4
0.0
0.1
0.0
-0.1
-0.1
0.0
0.0
-0.2
0.0
0.0
0.0
-0.1
0.0
0.0
0.0
-0.1
2.2E-02
2.3E-02
0.0E+00
3.6E-08
1.7E-05
4.2E-04
4.7E-04
7.1E-04
2.9E-03
3.9E-03
6.1E-03
1.5E-02
1.6E-02
1.9E-02
2.0E-02
2.4E-02
5.0E-02
6.8E-11
8.1E-11
1.7E-03
6.1E-03
6.4E-03
-0.7
-0.1
7.7E-03
0.3
0.5
-0.1
-0.1
3.7E-02
3.8E-02
-0.5
0.0
4.5E-02
0.7
-0.4
-0.2
0.1
0.0
0.2
2.3E-03
4.5E-03
1.3E-02