Fig. 9

The top three merged networks based on the 643 probe sets that were common between BCBM and prBT but significantly differentially expressed between BCBM and BC include molecules that are related to cancer, cell death and survival, organismal injury and abnormalities, hereditary disorder, neurological disease, carbohydrate and drug metabolism, and molecular transport. Molecules that are upregulated in BCBM compared to BC include, APLP1, C20orf24, CCNK, CLN8, COX4I1, COX5B, CRTC3, CSNK2A2, CWC15, EBAG9, FUNDC2, GCFC2, GTF2A2, HAUS1, HAUS2, LSM3, MLXIPL, MRPL40, MRPS21, MYL12B, NDRG1, NDUFAF3, NDUFS4, MRPS24, PCDHB14, PEBP1, PHLPP2, RNU4-2, RNU5B-1, RPL7A (SNORD36B), RPL13A (SNORD32A), RPL18A (SNORA68), RPL23A (SNORD42A), RPL27A (SNORA45A), RPL31, RPL36, SOD3, TAF1D, TAF9B, TIMM8B, TMEM223, TPGS2, TUBG1, UBE2R2, UBL5, UFC1. Downregulated molecules include ADAMTS1, AFAP1L2, AFG3L2, ALDH18A1, ARMCX3, AQP3, ATP6V1H, C15orf48, CAPG, CDK5RAP3, CPA3, EWSR1, FKBP3, FST, GOLT1B, GTF2H2C (paralogue GTF2H2C_2 in data set), HIST1H1D, HNRNPM, ITGA4, LBR, LY75 (LY75-CD302 readthrough in data set), MINOS1, MME, MRPL1, NDUFA4, NDUFA5, PDIA6, PLRG1, PNN, PRSS23, RPL5 (SNORD21), RPL22, SLC19A2, SLC25A6, SLC4A7, SNRPD3, TADA1, and UGCG. Integrative molecules comprise 60S ribosomal subunit, ADCY, Akt, Ck2, cytochrome-c oxidase, ERK, estrogen receptor, FSH, IL1, Importin beta, Lh, Mapk, mitochondrial complex 1, NADH dehydrogenase, Rar, Holo RNA polymerase II, RNA polymerase II, secretase gamma, snRNP, and Vegf. Asterisks mark molecules with more than one probe set. The pathway was overlaid with the Molecule Activity Predictor to precalculate further molecular effects, as outlined in the prediction legend