Proteomic-Based Biosignatures in Breast Cancer Classification and Prediction of Therapeutic Response

Table 5

Top 30 proteins predicting tumor response to neoadjuvant chemotherapy in TNBC tumors.

Rank	Protein name	Accession no.	R/IR + NR mean	Subcellular location	Function
1	Heat shock 70 kDa protein 8 isoform 1	gi∣5729877	0.32		Stress response
2	Periostin precursor (PN) (osteoblast-specific factor 2)	gi∣93138709	0.31	Nucleus	Transcription regulation
3	Cyclophilin A	gi∣1633054	0.41	Secreted	Cell attachment adhesion and spreading
4	Tyrosine 3/tryptophan 5-monooxygenase activation protein	gi∣5803225 (+1)	3.71	Nucleus	Protein binding
5	Profilin	gi∣157838211 (+4)	0.32	Cytoplasm, cytoskeleton	Actin cytoskeleton organization
6	Cardiac muscle alpha actin 1 proprotein	gi∣4885049	0.08	Cytoplasm, cytokeleton	actin filament-based movement, apoptosis
7	Beta actin	gi∣4501885	0.22	Cytoplasm, cytokeleton	Cell motility
8	Caldesmon (CDM)	gi∣2498204	0.42	Cytoplasm, cytokeleton	Actin- and myosin-binding protein
9	Tubulin 𝛽5	gi∣7106439	0.19	Cytosol	Major constituent of microtubules
10	Tropomyosin 2 (beta) isoform 1	gi∣42476296	0.11	Cytoplasm, cytokeleton	Binding to actin filaments
11	Actinin, 𝛼4	gi∣12025678	0.11	Nucleus, cytoplasm	Protein transport
12	Ras homolog gene family, member A (RhoA)	gi∣10835049 (+4)	0.33	Cytoplasm, cell membrane	Regulating a signal transduction pathway
13	Heterogeneous nuclear ribonucleoprotein K	gi∣13384620	0.33	Cytoplasm, nucleus	Pre-mRNA-binding proteins
14	Tubulin 𝛼1	gi∣6755901	0.36	Cytosol	Major constituent of microtubules
15	Tropomyosin 4	gi∣4507651	0.35	Cytoplasm, cytokeleton	Binds to actin filaments
16	Complement component 1 inhibitor precursor	gi∣73858568	4.57	Secreted	Complement pathway
17	ATP synthase, H+ transporting, mitochondrial F1 complex	gi∣4757810	0.43	Mitochondrion	Proton-transporting ATP synthase complex assembly
18	Calnexin precursor	gi∣10716563	0.42	Endoplasmic reticulum membrane, cell membrane	Calcium-binding protein
19	Eukaryotic translation elongation factor 1 alpha 1	gi∣4503471	0.29	Cytoplasm	Protein biosynthesis
20	Annexin I	gi∣4502101	0.25	Nucleus, cytoplasm, membrane	Calcium/phospholipid-binding protein
21	Triosephosphate isomerase 1	gi∣4507645 (+2)	0.35	Cytosol, nucleus	Fatty acid biosynthesis, gluconeogenesis, glycolysis, lipid synthesis
22	Cathepsin D preproprotein	gi∣4503143	0.35	Lysosome	proteolysis
23	Alpha glucosidase II alpha subunit isoform 2	gi∣38202257	0.19	Cytosol	Glycan metabolism, N-glycan metabolism
24	Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein	gi∣4507949 (+1)	0.42	Nucleus	Protein binding
25	Thymosin 𝛽10	gi∣10863895	0.42	Cytoplasm, cytokeleton	cytoskeleton organization
26	Aconitase 2 precursor	gi∣4501867	0.44	Mitochondrion	Carbohydrate metabolism, tricarboxylic acid cycle
27	Heterogeneous nuclear ribonucleoprotein D isoform a	gi∣14110420	0.48	Nucleus, cytoplasm	Transcription regulation
28	Serine (or cysteine) proteinase inhibitor	gi∣32454741	0.25	Secreted	Inhibits activated protein C, plasminogen activator
29	Lumican precursor	gi∣4505047	0.28	Secreted	Binds to laminin
30	Apolipoprotein D	gi∣619383	2.86	Secreted	Transport