Table 3.

Gene sets overexpressed in IBC compared with Non-IBC

GO category	GO term	Number of genes	GSA test P value
Gene sets overexpressed in ER+/HER2-normal IBC compared with Non-IBC
GO:0002675	Positive regulation of acute inflammatory response	11	0.001
GO:0002673	Regulation of acute inflammatory response	15	0.001
GO:0050729	Positive regulation of inflammatory response	31	0.001
GO:0050727	Regulation of inflammatory response	57	0.002
GO:0043407	Negative regulation of MAP kinase activity	40	0.003
GO:0031406	Carboxylic acid binding	17	0.005
GO:0045103	Intermediate filament-based process	25	0.005
GO:0010574	Regulation of vascular endothelial growth factor production	17	0.006
GO:0045104	Intermediate filament cytoskeleton organization	23	0.006
GO:0046928	Regulation of neurotransmitter secretion	12	0.007
GO:0033549	MAP kinase phosphatase activity	12	0.008
GO:0043500	Muscle adaptation	20	0.008
GO:0002526	Acute inflammatory response	97	0.008
GO:0014896	Muscle hypertrophy	15	0.009
GO:0042531	Positive regulation of tyrosine phosphorylation of STAT protein	22	0.009
GO:0051348	Negative regulation of transferase activity	92	0.009
GO:0033673	Negative regulation of kinase activity	86	0.010
Gene sets overexpressed in HER2-positive IBC compared with Non-IBC
GO:0051668	Localization within membrane	15	0.001
GO:0051084	‘de novo’ posttranslational protein folding	15	0.001
GO:0009119	Ribonucleoside metabolic process	15	0.001
GO:0043681	Protein import into mitochondrion	16	0.001
GO:0009168	Purine ribonucleoside monophosphate biosynthetic process	22	0.001
GO:0006458	‘de novo’ protein folding	23	0.001
GO:0019206	Nucleoside kinase activity	23	0.001
GO:0042994	Cytoplasmic sequestering of transcription factor	11	0.002
GO:0006626	Protein targeting to mitochondrion	30	0.002
GO:0009116	Nucleoside metabolic process	41	0.002
GO:0003729	mRNA binding	90	0.002
GO:0043094	Cellular metabolic compound salvage	10	0.003
GO:0051220	Cytoplasmic sequestering of protein	14	0.003
GO:0022884	Macromolecule transmembrane transporter activity	15	0.003
GO:0042273	Ribosomal large subunit biogenesis	18	0.003
GO:0010466	Negative regulation of peptidase activity	21	0.003
GO:0005758	Mitochondrial intermembrane space	34	0.003
GO:0046128	Purine ribonucleoside metabolic process	13	0.004
GO:0019201	Nucleotide kinase activity	30	0.004
GO:0008344	Adult locomotory behavior	35	0.004
GO:0019059	Initiation of viral infection	42	0.004
GO:0006446	Regulation of translational initiation	72	0.004
GO:0015935	Small ribosomal subunit	89	0.004
GO:0030159	Receptor signaling complex scaffold activity	24	0.005
GO:0031970	Organelle envelope lumen	41	0.005
GO:0046148	Pigment biosynthetic process	54	0.007
GO:0015934	Large ribosomal subunit	99	0.007
GO:0006144	Purine base metabolic process	24	0.008
GO:0009146	Purine nucleoside triphosphate catabolic process	13	0.009
GO:0042274	Ribosomal small subunit biogenesis	22	0.009
GO:0009161	Ribonucleoside monophosphate metabolic process	33	0.009
GO:0006195	Purine nucleotide catabolic process	20	0.010
GO:0030041	Actin filament polymerization	81	0.010
Gene sets overexpressed in ER-negative/HER2-normal IBC compared with Non-IBC
GO:0035094	Response to nicotine	19	0.001
GO:0043279	Response to alkaloid	27	0.001
GO:0005548	Phospholipid transporter activity	35	0.001
GO:0048545	Response to steroid hormone stimulus	97	0.001
GO:0006800	Oxygen and reactive oxygen species metabolic process	78	0.002
GO:0002437	Inflammatory response to antigenic stimulus	14	0.003
GO:0005100	Rho GTPase activator activity	26	0.003
GO:0014902	Myotube differentiation	16	0.004
GO:0016528	Sarcoplasm	34	0.004
GO:0008367	Bacterial binding	12	0.005
GO:0014070	Response to organic cyclic substance	37	0.006
GO:0043627	Response to estrogen stimulus	62	0.006
GO:0002861	Regulation of inflammatory response to antigenic stimulus	13	0.007
GO:0048019	Receptor antagonist activity	14	0.008
GO:0016529	Sarcoplasmic reticulum	33	0.008
GO:0007631	Feeding behavior	41	0.008
GO:0002683	Negative regulation of immune system process	71	0.009
GO:0006656	Phosphatidylcholine biosynthetic process	13	0.010