Background: Breast cancer is the most common cancer in women across the world, with
high incidence and mortality rates. Being a heterogeneous disease, gene expression profiling based
analysis plays a significant role in understanding breast cancer. Since expression patterns of patients
belonging to the same stage of breast cancer vary considerably, an integrated stage-wise analysis involving
multiple samples is expected to give more comprehensive results and understanding of breast
Objective: The objective of this study is to detect functionally significant modules from gene coexpression
network of cancerous tissues and to extract prognostic genes related to multiple stages of
Methods: To achieve this, a multiplex framework is modelled to map the multiple stages of breast cancer,
which is followed by a modularity optimization method to identify functional modules from it.
These functional modules are found to enrich many Gene Ontology terms significantly that are associated
Results and Discussion: Predictive biomarkers are identified based on differential expression analysis
of multiple stages of breast cancer.
Conclusion: Our analysis identified 13 stage-I specific genes, 12 stage-II specific genes, and 42 stage-
III specific genes that are significantly regulated and could be promising targets of breast cancer therapy.
That apart, we could identify 29, 18 and 26 lncRNAs specific to stage I, stage II and stage III, respectively.