A computer-implemented method for inferring activity of a TGF-β cellular signaling pathway in a subject performed by a digital processing device, wherein the inferring comprises: receiving expression levels of three or more target genes of the TGF-β cellular signaling pathway measured in a sample of the subject, determining an activity of the TGF-β cellular signaling pathway based on evaluating a calibrated mathematical pathway model relating the expression levels of the three or more TGF-β target genes to an activity level of the family of TGF-β transcription factor elements, the family of TGF-β TF elements controlling transcription of the three or more TGF-β target genes, the activity of the TGF-β cellular signaling pathway being defined by the activity level of the family of TGF-β TF elements, the calibrated mathematical pathway model being a model that is calibrated using a ground truth dataset including samples in which transcription of the three or more TGF-β target genes is induced by the family of TGF-β TF elements and samples in which transcription of the three or more TGF-β target genes is not induced by the family of TGF-β TF elements, wherein the three or more TGF-β target genes are selected from the group consisting of: ANGPTL4, CDC42EP3, CDKN1A, CDKN2B, CTGF, GADD45A, GADD45B, HMGA2, ID1, IL11, INPP5D, JUNB, MMP2, MMP9, NKX2-5, OVOL1, PDGFB, PTHLH, SERPINE1, SGK1, SKIL, SMAD4, SMAD5, SMAD6, SMAD7, SNAI1, SNAI2, TIMP1, and VEGFA, preferably, from the group consisting of: ANGPTL4, CDC42EP3, CDKN1A, CTGF, GADD45A, GADD45B, HMGA2, ID1, IL11, JUNB, PDGFB, PTHLH, SERPINE1, SGK1, SKIL, SMAD4, SMAD5, SMAD6, SMAD7, SNAI2, and VEGFA, more preferably, from the group consisting of: ANGPTL4, CDC42EP3, CDKN1A, CTGF, GADD45B, ID1, IL11, JUNB, PDGFB, SERPINE1, SKIL, SMAD7, SNAI2, and VEGFA, most preferably, from the group consisting of: ANGPTL4, CDC42EP3, ID1, IL11, JUNB, SERPINE1, SKIL, and SMAD7, wherein the TGF-β cellular signaling pathway refers to a signaling process that leads to transcriptional activity of the family of TGF-β TF elements, and wherein the family of TGF-β TF elements are protein complexes each containing a dimer of one member selected from the group consisting of SMAD1, SMAD2, SMAD3, SMAD5 and SMAD8 with SMAD4 or a trimer of two members selected from the group consisting of SMAD1, SMAD2, SMAD3, SMAD5 and SMAD8 with SMAD4. receiving expression levels of three or more target genes of the TGF-β cellular signaling pathway measured in a sample of the subject, determining an activity of the TGF-β cellular signaling pathway based on evaluating a calibrated mathematical pathway model relating the expression levels of the three or more TGF-β target genes to an activity level of the family of TGF-β transcription factor elements, the family of TGF-β TF elements controlling transcription of the three or more TGF-β target genes, the activity of the TGF-β cellular signaling pathway being defined by the activity level of the family of TGF-β TF elements, the calibrated mathematical pathway model being a model that is calibrated using a ground truth dataset including samples in which transcription of the three or more TGF-β target genes is induced by the family of TGF-β TF elements and samples in which transcription of the three or more TGF-β target genes is not induced by the family of TGF-β TF elements, wherein the three or more TGF-β target genes are selected from the group consisting of: ANGPTL4, CDC42EP3, CDKN1A, CDKN2B, CTGF, GADD45A, GADD45B, HMGA2, ID1, IL11, INPP5D, JUNB, MMP2, MMP9, NKX2-5, OVOL1, PDGFB, PTHLH, SERPINE1, SGK1, SKIL, SMAD4, SMAD5, SMAD6, SMAD7, SNAI1, SNAI2, TIMP1, and VEGFA, preferably, from the group consisting of: ANGPTL4, CDC42EP3, CDKN1A, CTGF, GADD45A, GADD45B, HMGA2, ID1, IL11, JUNB, PDGFB, PTHLH, SERPINE1, SGK1, SKIL, SMAD4, SMAD5, SMAD6, SMAD7, SNAI2, and VEGFA, more preferably, from the group consisting of: ANGPTL4, CDC42EP3, CDKN1A, CTGF, GADD45B, ID1, IL11, JUNB, PDGFB, SERPINE1, SKIL, SMAD7, SNAI2, and VEGFA, most preferably, from the group consisting of: ANGPTL4, CDC42EP3, ID1, IL11, JUNB, SERPINE1, SKIL, and SMAD7, wherein the TGF-β cellular signaling pathway refers to a signaling process that leads to transcriptional activity of the family of TGF-β TF elements, and wherein the family of TGF-β TF elements are protein complexes each containing a dimer of one member selected from the group consisting of SMAD1, SMAD2, SMAD3, SMAD5 and SMAD8 with SMAD4 or a trimer of two members selected from the group consisting of SMAD1, SMAD2, SMAD3, SMAD5 and SMAD8 with SMAD4.