title: Computational exploration of the activated pathways associated with DNA damage response in breast cancer.
abstract: Molecular signaling events regulate cellular activity. Cancer stimulating signals trigger cellular responses that evade the regulatory control of cell development. To understand the mechanism of signaling regulation in cancer, it is necessary to identify the activated pathways in cancer. We have developed RepairPATH, a computational algorithm that explores the activated signaling pathways in cancer. The RepairPATH integrates RepairNET, an assembled protein interaction network associated with DNA damage response, with the gene expression profiles derived from the microarray data. Based on the observation that cofunctional proteins often exhibit correlated gene expression profiles, it identifies the activated signaling pathways in cancer by systematically searching the RepairNET for proteins with significantly correlated gene expression profiles. Analyzing the gene expression profiles of breast cancer, we found distinct similarities and differences in the activated signaling pathways between the samples from the patients who developed metastases and the samples from the patients who were disease free within 5 years. The cellular pathways associated with the various DNA repair mechanisms and the cell-cycle checkpoint controls are found to be activated in both sample groups. One of the most intriguing findings is that the pathways associated with different cellular processes are functionally coordinated through BRCA1 in the disease-free sample group, whereas such functional coordination is absent in the samples from patients who developed metastases. Our analysis revealed the potential cellular pathways that regulate the signaling events in breast cancer.
authors.affiliation: Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA.
authors.forename: Liting
authors.initials: L
authors.lastname: Wen
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Marc
authors.initials: M
authors.lastname: Sobel
authors.forename: Jin-an
authors.initials: JA
authors.lastname: Feng
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000503:physiopathology*; D016203:CDC2 Protein Kinase / Q000502:physiology; D002135:Calcium-Binding Proteins / Q000502:physiology; D064199:Cdc20 Proteins; D018797:Cell Cycle Proteins / Q000502:physiology; D019295:Computational Biology; D019925:Cyclin A / Q000502:physiology; D004249:DNA Damage / Q000502:physiology*; D004260:DNA Repair / Q000502:physiology*; D020869:Gene Expression Profiling; D006801:Humans; D064246:Mad2 Proteins; D009362:Neoplasm Metastasis; D020411:Oligonucleotide Array Sequence Analysis; D025941:Protein Interaction Mapping; D051818:Replication Protein C / Q000502:physiology; D012097:Repressor Proteins / Q000502:physiology; D015398:Signal Transduction
chemical_list: D002135:Calcium-Binding Proteins; D064199:Cdc20 Proteins; D018797:Cell Cycle Proteins; D019925:Cyclin A; C577697:MAD2L1 protein, human; D064246:Mad2 Proteins; C497563:RFC4 protein, human; D012097:Repressor Proteins; C577488:CDC20 protein, human; D016203:CDC2 Protein Kinase; D051818:Replication Protein C