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The immune system is essential for host defense to pathogen infection, tissue repair, stress response, and other physiological functions. An unbalanced immune system is detrimental to homeostasis and mammalian survival. Immunodeficiency can cause susceptibility to pathogen infection. A hyperactive immune system can cause autoimmunity and chronic inflammatory diseases including rheumatoid arthritis, psoriasis, and atherosclerosis. Deciphering the mechanisms regulating the immune response will illuminate on the pathogenesis of inflammatory diseases and promote the development of new therapies to treat these diseases. Because innate immunity is the first line of host defense and transcription is a critical contributor to the innate immune response, we focused our studies on mechanisms regulating transcriptional activation of the innate immune response. Toll-like receptor (TLR) signaling is a classical model to study pathogen recognition and the activation of innate immunity. TLR transcriptional cascades have been extensively studied using conventional systems approaches. Because conventional systems approaches rely on statistics and large sample sizes to uncover the common regulatory mechanisms, they often miss gene-specific regulatory mechanisms. To reveal gene-specific regulatory mechanisms, we used a stringent systems approach to dissect the TLR transcriptional cascades in chapter 2. To prevent biases towards the majority of weakly induced genes, we separated strongly induced genes from weakly induced genes. Combining high-resolution transcriptional profiles and perturbation studies, we classified TLR4-activated genes by their activation mechanisms. By integrating RNA-seq, ChIP-seq, ATAC-seq, and motif data, we found that several key inflammatory genes are regulated by highly selective mechanisms. TLR4-activated nuclear factor kappa B (NFκB) and interferon regulatory factor 3 (IRF3) selectively regulate a small subset of pro-inflammatory genes by chromatin and combinatorial regulation. We also found serum response factor (SRF) selectively regulates a few early transient primary response genes. In chapter 3, we used a gene-centric method and identified the motif rules governing the combinatorial regulation of serum response factor (SRF) and ternary complex factor (TCF). Ternary complex formation can enhance SRF binding and promote histone mark deposition. The active ternary complex can regulate transcription through either promoter or enhancer. Taken together, we demonstrated a gene-centric, stringent systems approach that can complement the conventional systems approach to unveil gene-specific regulatory mechanisms in ligand-induced transcriptional cascades.