Gene expression

• LCL
• Fibroblasts
• THP-1

Ground truth networks

• ChIP-seq
• LCL
• Fibroblasts
• THP-1
• TF knockdown
• LCL
• THP-1
• Functional binding
• LCL
• THP-1

TF binding motif network

• P-value network (P-value weighted adjacency matrix; FIMO threshold p-value 1e-3)
• 0.5 threshold FDR-corrected network (Adjacency matrix)
• old motif (pairs format)

TF-TF PPI

• TF-TF PPI with direct combined edges
• TF-TF PPI with first neighbor combined edges
• TF-TF PPI with second neighbor combined edges
• TF-TF PPI with third neighbor combined edges
• TF-TF PPI with fourth neighbor combined edges
• TF-TF PPI with direct binding edges
• TF-TF PPI with first neighbor binding edges
• TF-TF PPI with second neighbor binding edges
• TF-TF PPI with third neighbor binding edges
• TF-TF PPI with fourth neighbor binding edges

Benchmark results

• ChIP-seq
• PANDA:LCL
• optPANDA:LCL
• PANDA:Fibroblast
• optPANDA:Fibroblast
• PANDA:THP-1
• optPANDA:THP-1
• TF knockdown
• PANDA:LCL
• optPANDA:LCL
• PANDA:THP-1
• optPANDA:THP-1
• Functional binding
• PANDA:LCL
• optPANDA:LCL
• PANDA:THP-1
• optPANDA:THP-1