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Ingenuity Pathway Analysis (IPA) is an industry-leading software tool for pathway, function, interaction network analysis. It should be your first choice in analyzing the biological impacts of gene expression, miRNA expression, metabolomics, and proteomics data.
BIOBASE/TRANSFAC database features one of the largest collection of eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. Use this tool to identify potential transcription factors targeting your gene(s).