Pseudogenes (y) are genomic DNA sequences homologous to functional genes but are not translated into protein. Although once considered as genomic fossils, the transcribed pseudogenes (TPGs) in mice and flies are now known to function as gene regulators through generation of endogenous small interfering RNAs (esiRNAs), antisense RNAs, or RNA decoys. Postulating that pseudogenes may generate esiRNAs to regulate gene expression in human genome, as in animal models, we performed a genome-wide analysis to explore the siRNA-mediated mechanisms of pseudogenes.
PseudoMap is a resource of exploring the relationships between TPG and its cognate with miRNA decoyed mechanism and TPG-derived esiRNA-target interactions. This site with four major differentiating features is distinct from these published on-line public databases. First, we identify the TPGs and provide the expression profiles for TPGs and their cognates. Second, we provide the miRNA regulators of TPGs as well as their parental genes. Third, we also detect the TPG-derived esiRNAs as supported by any amount of Illumina-Solexa reads. Finally, we construct the interactions of TPG-derived esiRNAs as well as their interacting gene targets in the human genome. The following is flowchart: