Table II. Expression profiles of the top 65 gene products screened at both protein and transcript level and of 30 additional transcripts based on the literature in all breast cancer immnophenotypes involved in the study. Proteins with low number of observations (N ≤ 10) in the proteomics study are in italics (see Experimental procedures for details). Agreements in statistically significant changes at protein and transcript levels are indicated in bold. Up = up-regulation, down = down-regulation. Gene products monitored only at transcript level are underlined.

G1: N1–2/N0
Protein	up: CPB1, GIT2, SFN, RNF25, OGFR, TMSB10, RELA, PDLIM2, THBS2, STMN1, TPM4, YWHAH ‖ down: KNG1, CALML5, PLG
Transcript	up: RNF25, TRAF3IP2, PPP5C, PDLIM2, RELA, TIMP1, YWHAH, CPB1, RAB13, ITGAV, AGR3, CDH5, TMSB10, STMN1 ‖ down: -
G3: N1–2/N0
Protein	up: CALB2, SFRP2, MTMR15, TRAF3IP2, CD9, COL19A1, EPPK1, POSTN, TGFBI, S100A10, TPM2, S100A11, PGRMC2, ACTN4, ANXA1, STAT3, CALD1, LAMB2, PTMS, ITGB1, TAGLN ‖ down: S100A9
Transcript	up: SERPINE1, ITGB1, THBS2, SPP1, CGN, LAMB2 ‖ down: -
N1–2/N0
Protein	up: SFRP2, TRAF3IP2, COL19A1, RNF25, OGFR, ITGAV, TPM2, TPM4, LAMB2 ‖ down: -
Transcript	up: TRAF3IP2, SERPINE1, CFL1, CGN, ITGB1, ANXA1, TPM4, RAB13, POSTN, SPP1 ‖ down: -
N1–2: G3/G1
Protein	up: CALML5, CALB2, S100A9, AHSA1, CFL1, S100A4, ANXA1, ACTB ‖ down: CPB1, THBS4, CLIC6, CCDC41, COL19A1, AGR3, EDAR, PDLIM2, TP53RK, POSTN, TPM2, THBS2, TRAF3IP2, SFN, MTA3, TAGLN, TPM4, YWHAH, LAMB2
Transcript	up: STMN1, MMP9, MMP1, TMSB10, S100A9, EPCAM, CASP14 ‖ down: LAMB2, ESR1, TIMP1, PGR, HGF, CLIC6, ITGAV, ERBB3, MUC1, RNF25, CPB1, AGR3, MTA3, ALCAM, POSTN, RAB13, FLT4, SFRP2, MTMR15, CDH5, PGRMC2, CGN, TRAF3IP2, VEGFC, GIT2, STAT3, AGR2, GSN, THBS10, CCDC41, CRIP1, FLT1, CD44, PPP5C, THBS2, CASP14
N0: G3/G1
Protein	up: S100A9, TMSB10, SERBP1, S100A4, STMN1 ‖ down: CLIC6, POSTN, CRIP1, TRAF3IP2, COL19A1, TAGLN, EPPK1, TPM2, KNG1, TP53RK, RBP4, THBS4, CALD1, S100A10, ITGB1, ITGAV, VIM, LAMB2, PLG, PTMS, RAB13, GSN, CCDC41, TGFBI, THBS2
Transcript	up: COL19A1, TMSB10, FASLG, STMN1, S100A9, YWHAH, MMP9, MMP1, CXCR4, RELA, S100A4, OGFR, CASP14, PDLIM2 ‖ down: LAMB2, PGR, CLIC6, MUC1, SFRP2, POSTN, STAT3, THBS2, ERBB3, ESR1, CRIP1, ALCAM, TAGLN, CGN, AGR3, GSN, MTA3, THBS4, ITGAV, RAB13, HGF, TPM4, ITGB1, TIMP1, TPM2, AGR2
G3/G1
Protein	up: S100A9, CALML5, SUSD2, S100A4, TMSB10, CFL1, SERBP1, AHSA1 ‖ down: THBS4, POSTN, COL19A1, CRIP1, CCDC41, TRAF3IP2, AGR3, TP53RK, TPM2, TAGLN, PDLIM2, EPPK1, RBP4, EDAR, THBS2, CALD1, S100A10, ITGAV, LAMB2, MTA3, TPM4
Transcript	up: STMN1, TMSB10, MMP9, MMP1, S100A9, FASLG, COL19A1, CASP14, EPCAM, CXCR4, YWHAH, AHSA1, OGFR, EGFR, MET ‖ down: LAMB2, PGR, CLIC6, ERBB3, ESR1, SFRP2, POSTN, AGR3, TIMP1, ALCAM, ITGAV, HGF, MTA3, STAT3, THBS2, CGN, RAB13, CRIP1, RNF25, GSN, THBS4, FLT4, MTMR15, AGR2, TAGLN, GIT2, VEGFC, CCDC41, TPM4, CPB1, PGRMC2, MMP11, CDH5, CD9, TPM2
ER+/ER-
Protein	up: AGR2, CRIP1, CLIC6, CPB1, AGR3, THBS4, EDAR, COL19A1, CCDC41, TP53RK, PTMS, SUSD2, POSTN, MTA3, ALCAM, CGN, TRAF3IP2, TPM2, TAGLN, EPPK1, TPM4, THBS2 ‖ down: CASP14, S100A9, CALML5, S100A4
Transcript	up: ESR1, CRIP1, AGR3, ERBB3, PGR, AGR2, PPP5C, CGN, CPB1, RNF25, MTA3, ALCAM, MTMR15, PGRMC2, CDH1, THBS4, PTMS, LAMB2, GIT2, OGFR, CDK5RAP3, CLIC6, RAB13 ‖ down: CD82, EGFR, S100A9, S100A10, ANXA1, VIM, MMP1, S100A6, CALD1, CALB2
HER2+/HER2-
Protein	up: ERBB2, CRIP1, SUSD2, KNG1 ‖ down: CLIC6, THBS4, SFN, PDLIM2, EDAR, S100A6, STMN1, PTMS
Transcript	up: ERBB2, SUSD2, MUC1, CDH1, TMSB10, TP53RK, S100A11, MMP11, CD9, POSTN, EPPK1, GIT2, KISS1, TRAF3IP2, PGRMC2, CASP14, RAB13, AGR2, MTA3 ‖ down: -
TN/LA
Transcript only	up: TMSB10, S100A9, EGFR, MMP1, FASLG, COL19A1, CD82, MMP9, STMN1, EDAR, MET, ANXA1, S100A10, CASP14 ‖ down: ESR1, PGR, CLIC6, MTA3, LAMB2, POSTN, AGR3, CRIP1, ERBB3, AGR2, ERBB2, MTMR15, CPB1, MUC1, ALCAM, THBS2, CGN, ITGAV, RNF25, PGRMC2, FLT4, MMP11, RAB13, THBS4, SFRP2, STAT3, GIT2, VEGFC, FASLG, HGF, TPM4, CD9, PPP5C, TAGLN, TRAF3IP2, CCDC41, TIMP1, TP53RK, SUSD2, GSN, CDH1