Table II GO terms and curated gene sets enrichment of selected BRCA signatures
Top enriched GO termsTop enriched curated sets
NegativePositiveNegativePositive
Clinically relevant signatures (significant total count >25)
    pr_02GO_MYOSIN_II_COMPLEXGO_ERBB2_SIGNALING_PATHWAYREACTOME_RESPIRATORY_ELECTRON_TRANSPORTSMID_BREAST_CANCER_ERBB2_UP
    pr_04GO_BRANCHED_CHAIN_AMINO_ACID_METABOLIC_PROCESSGO_DNA_REPLICATIONWOO_LIVER_CANCER_RECURRENCE_DNDUTERTRE_ESTRADIOL_RESPONSE_24HR_UP
    pr_18GO_CILIARY_TIPGO_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_THE_CH_OH_GROUP_OF_DONORS_NAD_OR_NADP_AS_ACCEPTORSMID_BREAST_CANCER_LUMINAL_B_UPREACTOME_GLUCOSE_METABOLISM
    pr_29GO_MITOCHONDRIAL_TRANSLATIONGO_ANCHORED_COMPONENT_OF_MEMBRANEREACTOME_LIPOPROTEIN_METABOLISMDOANE_BREAST_CANCER_ESR1_UP
    pr_48GO_ACTIN_MYOSIN_FILAMENT_SLIDINGGO_CELLULAR_MONOVALENT_INORGANIC_CATION_HOMEOSTASISREACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_SMID_BREAST_CANCER_BASAL_UP
    pr_49GO_MICROBODY_LUMENGO_RIBOSOME_BIOGENESISSMID_BREAST_CANCER_BASAL_DNCAIRO_HEPATOBLASTOMA_CLASSES_UP
    tx_07GO_CYTOSOLIC_LARGE_RIBOSOMAL_SUBUNITGO_EMBRYONIC_HINDLIMB_MORPHOGENESISWANG_LSD1_TARGETS_DNMIKKELSEN_NPC_HCP_WITH_H3K27ME3
    tx_19GO_NECROPTOTIC_PROCESSGO_OLIGODENDROCYTE_DIFFERENTIATIONKOHOUTEK_CCNT1_TARGETSNIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLICON
    tx_21GO_RESPONSE_TO_PHGO_STEROID_BINDINGSMID_BREAST_CANCER_BASAL_UPDOANE_BREAST_CANCER_ESR1_UP
    tx_31GO_VASODILATIONGO_MHC_PROTEIN_COMPLEXBIOCARTA_NO1_PATHWAYICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_DN
    tx_34GO_VOLTAGE_GATED_CALCIUM_CHANNEL_COMPLEXGO_MUSCLE_CELL_MIGRATIONVANTVEER_BREAST_CANCER_METASTASIS_UPLIN_SILENCED_BY_TUMOR_MICROENVIRONMENT
    tx_40GO_REGULATION_OF_ENDOCRINE_PROCESSGO_EPIDERMIS_DEVELOPMENTNIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICONTURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN
    tx_46GO_NEGATIVE_REGULATION_OF_CALCIUM_ION_TRANSPORTGO_CHROMOSOME_SEGREGATIONSOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_DNDUTERTRE_ESTRADIOL_RESPONSE_24HR_UP
    tx_63GO_CALCIUM_DEPENDENT_CELL_CELL_ADHESION_VIA_PLASMA_MEMBRANE_CELL_ADHESION_MOLECULESGO_CILIUM_ORGANIZATIONNIKOLSKY_BREAST_CANCER_16Q24_AMPLICONCREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2
    tx_64GO_INNER_EAR_RECEPTOR_CELL_DEVELOPMENTGO_POSITIVE_REGULATION_OF_INTERLEUKIN_2_PRODUCTIONPID_WNT_SIGNALING_PATHWAYTSUNODA_CISPLATIN_RESISTANCE_DN
    tx_72GO_PROTEIN_LIPID_COMPLEXGO_NEUROEPITHELIAL_CELL_DIFFERENTIATIONFARMER_BREAST_CANCER_CLUSTER_3MASSARWEH_TAMOXIFEN_RESISTANCE_DN
Consistent signatures (cluster silhouette >0.9)
    pr_33GO_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_NONSENSE_MEDIATED_DECAYGO_IRON_ION_BINDINGREACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANEJAATINEN_HEMATOPOIETIC_STEM_CELL_DN
    pr_45GO_TRANSLATIONAL_TERMINATIONGO_LYMPHOCYTE_ACTIVATIONCHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UPWALLACE_PROSTATE_CANCER_RACE_UP
    pr_15GO_VOLTAGE_GATED_ION_CHANNEL_ACTIVITYGO_BLOOD_MICROPARTICLEREACTOME_PERK_REGULATED_GENE_EXPRESSIONHSIAO_LIVER_SPECIFIC_GENES
    pr_25GO_DNA_PACKAGING_COMPLEXGO_CONTRACTILE_FIBERABRAMSON_INTERACT_WITH_AIREREACTOME_MUSCLE_CONTRACTION
    pr_61GO_TUBE_FORMATIONGO_LIPID_PARTICLENIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLICONNAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN
    pr_08GO_SNRNA_METABOLIC_PROCESSGO_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORKKEGG_RNA_DEGRADATIONMILI_PSEUDOPODIA_HAPTOTAXIS_DN
    pr_54GO_FATTY_ACID_BINDINGGO_DEFENSE_RESPONSE_TO_VIRUSREACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNATAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_UP
    pr_63GO_GOLGI_VESICLE_TRANSPORTGO_TRANSFERASE_ACTIVITY_TRANSFERRING_ALKYL_OR_ARYL_OTHER_THAN_METHYL_GROUPSLEE_LIVER_CANCER_CIPROFIBRATE_UPKEGG_DRUG_METABOLISM_CYTOCHROME_P450
    pr_04GO_BRANCHED_CHAIN_AMINO_ACID_METABOLIC_PROCESSGO_DNA_REPLICATIONWOO_LIVER_CANCER_RECURRENCE_DNDUTERTRE_ESTRADIOL_RESPONSE_24HR_UP
    pr_31GO_PHOSPHOLIPID_BIOSYNTHETIC_PROCESSGO_DNA_PACKAGINGKEGG_DRUG_METABOLISM_OTHER_ENZYMESWAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_DN
    pr_39GO_ORGANELLAR_LARGE_RIBOSOMAL_SUBUNITGO_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_NONSENSE_MEDIATED_DECAYZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UPREACTOME_PEPTIDE_CHAIN_ELONGATION
    tx_46GO_NEGATIVE_REGULATION_OF_CALCIUM_ION_TRANSPORTGO_CHROMOSOME_SEGREGATIONSOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_DNDUTERTRE_ESTRADIOL_RESPONSE_24HR_UP
    tx_48GO_BICARBONATE_TRANSPORTGO_PROTEINACEOUS_EXTRACELLULAR_MATRIXMOOTHA_HUMAN_MITODB_6_2002ANASTASSIOU_CANCER_MESENCHYMAL_TRANSITION_SIGNATURE
    tx_43GO_NUCLEOTIDE_PHOSPHORYLATIONGO_ADAPTIVE_IMMUNE_RESPONSESMID_BREAST_CANCER_LUMINAL_B_UPSMID_BREAST_CANCER_NORMAL_LIKE_UP
    tx_28GO_TRANSLATIONAL_INITIATIONGO_SODIUM_CHANNEL_ACTIVITYHSIAO_HOUSEKEEPING_GENESGINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN
    tx_52GO_CYTOSOLIC_RIBOSOMEGO_DEFENSE_RESPONSE_TO_VIRUSREACTOME_PEPTIDE_CHAIN_ELONGATIONHECKER_IFNB1_TARGETS
    tx_49GO_RIBOSOMAL_SUBUNITGO_HELICASE_ACTIVITYREACTOME_PEPTIDE_CHAIN_ELONGATIONGABRIELY_MIR21_TARGETS
    tx_30GO_REGULATION_OF_MESENCHYMAL_CELL_PROLIFERATIONGO_INFLAMMATORY_RESPONSESENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_DNMCLACHLAN_DENTAL_CARIES_UP
    tx_63GO_CALCIUM_DEPENDENT_CELL_CELL_ADHESION_VIA_PLASMA_MEMBRANE_CELL_ADHESION_MOLECULESGO_CILIUM_ORGANIZATIONNIKOLSKY_BREAST_CANCER_16Q24_AMPLICONCREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2
    tx_23GO_POSITIVE_REGULATION_OF_MESENCHYMAL_CELL_PROLIFERATIONGO_LIPID_PARTICLEMUELLER_METHYLATED_IN_GLIOBLASTOMANAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN