Transcranial magnetic stimulation (TMS) is gaining increasing attention for therapeutic treatment of mental illnesses. However, a clear understanding of its impact to the underlying brain mechanisms is critical for its effective application. For this, we analyze electroencephalography (EEG) response to TMS subthreshold pulse at the left motor cortex from 6 healthy controls and 6 schizophrenia patients. We use principal component analysis (PCA) along sparse nonnegative matrix factorization (NMF), an unsupervised machine learning technique, on brain connectivity data established by sliding window coherence of EEG based source localized data. The source localization was achieved by using the sLORETA algorithm on our EEG data after artifact removal. This, hence, provides high temporal and spatial resolution in the connectivity analysis results, giving advantage over other neuroimaging modalities. PCA aids in establishing the number of common underlying connected subnetworks (say k) across subjects whereas NMF is employed to derive these k spatial and temporal signature subnetwork response to the stimulus. Within these signatures, we studied motor cortical connectivity and found that schizophrenia patients exhibited sensory gating deficits as compared to controls. These findings can act as potential biomarkers to monitor TMS for clinical therapeutic techniques in the future.