The presence of uncharacterized loci (LOC101927588) and non-coding RNAs among the most connected genes highlights the potential involvement of previously unrecognized regulatory mechanisms in PCOS pathophysiology, while the inclusion of immune-related (ITK) and developmental (SOX3, SPO11) factors underscores the multi-system nature of pioglitazone’s molecular effects in treating this complex endocrine disorder. This evidence concerns the gene SOX3 and endocrine system disorder.