Table 3.
Differentially expressed pathway gene sets.
| Basal | ERBB2 | Lum A | Lum B | Normal |
|---|---|---|---|---|
| Up-regulated | ||||
|
CELL CYCLE(6) DNA_REPLICATION(3) tRNA SYNTHESIS(2) ACTINY TNF APOPTOSIS(2) CELL_ADHESION PROTEASOME ATRBRCA P53 SIGNALING IL12(2) TH1TH2 ST_B_CELL_ ANTIGEN_RECEPTOR ST_T_CELL_SIGNAL_ TRANSDUCTION ANTIGEN_PROCESSING/ PRES.TOLL_LIKE_ RECEPTOR NATURAL_ KILLER_CELL_CYTOTOX PI3K GLYCOSPHINGOLIPID_ BIOSYNTH ST_FAS_SIGNALING |
BIOSYNTHESIS_OF_ STEROIDS(2) PROTEASOME(2) ARGININE/PROLINE_ METABOLISM |
AMINO ACID METABOLISM(4) ST_JNK_MAPK CIRCADIAN_EXERCISE NITROGEN_ METABOLISM(2) BUTANOATE_ METABOLISM(2) PROPANOATE_ METABOLISM ESTROGEN_SIGNALING SPHINGOLIPID_ METABOLISM FATTY_ACID_ METABOLISM AKT IGF1 GLYCOSPHINGOLIPID_ METABOLISM VIP NUCLEAR_RECEPTORS GLEEVEC CARM_ER PDGF |
OXIDATIVE_ PHOSPHORYLATION(3) MPR P53 PROTEASOME(2) FRUCTOSE/MANNOSE_ METABOLISM(2) IGF1(2) PTDIN DNA_REPLICATION(3) CELL_CYCLE TRANSCRIPTION RAS CARM_ER CHREBP EIF4 RACCYCD BIOSYNTHESIS_OF_ STEROIDS CERAMIDE AMINO_ACID_ METABOLISM(2) CREB |
FATTY_ACID_METABOLISM HISTIDINE_METABOLISM MAPK_SIGNALING WNT_SIGNALING(3) FOCAL_ADHESION ECM PROSTAGLANDIN CARDIACEG ALK PDGF PPARA NUCLEAR_RECEPTORS EGF TGF_BETA_SIGNALING COMPLEMENT_CASCADE(2) SMOOTH_MUSCLE_ CONTRACTION RIBOSOMAL_PROTEINS IGF1 SPRY INTRINSIC |
| Down-regulated | ||||
| TEL MTOR(2) IGF1(2) GPCR VIP AMINO ACID METABOLISM(2) ESTROGEN_ SIGNALING NUCLEAR_ RECEPTORS CHREBP CERAMIDE CARM_ER GLYCOSPHINGOLIPID_ METABOLISM ST_JNK_MAPK BAD |
TEL GLEEVEC IGF1 NITROGEN_ METABOLISM(2) |
CELL_CYCLE(6) IL12(2) GLYCOLYSIS PENTOSE_ PHOSPHATE_(2) PROTEASOME ST_B_CELL_ANTIGEN_ RECEPTOR PTDINS DNA_REPLICATION(3) tRNA_SYNTHESIS(2) ST_T_CELL_SIGNAL_ TRANSDUCTION ACTINY CELL_ADHESION P53_SIGNALING NATURAL_KILLER_ CELL_CYTOTOX |
PROSTAGLANDIN_ SYNTHESIS NTHI ACTIN_ CYTOSKELETON GLYCEROLIPID_ METABOLISM IL1R TOLL LYSINE_DEGRADATION MELANOGENESIS FOCAL_ADHESION WNT_SIGNALING ALK CELL_ADHESION(2) CYTOKINE UREA_CYCLE |
CELL_CYCLE(5) DNA_REPLICATION(5) PENTOSE_PHOSPHATE(2) TRNA_BIOSYNTHESIS(2) OXIDATIVE_ PHOSPHORYLATION(3) CITRATE_CYCLE(3) PROTEASOME(3) GLYCOLYSIS P53 BIOSYNTHESIS_OF_ STEROIDS(2) ATRBRCA ST_FAS_SIGNALING GLUTAMATE_METABOLISM SELENOAMINO_ACID_ METABOLISM RACCYCD MPR |
Notes: Gene sets in bold were also significant in test data set (Mainz). The number of redundant pathway gene sets is given in brackets.