Genomewide Analysis of Phosphatase Gene Family in Humans

Protein tyrosine phosphatases (PTPs) cooperate with protein tyrosine kinases to regulate signal transduction pathways. IOB scientists carried out a bioinformatics analysis of protein tyrosine phosphatases in the human genome to examine the entire gene family including domain architecture, pseudogene analysis and alternative splicing (novel exons, skipped exons as well as cryptic donor/acceptor splice sites). The study involved a comparative genomic analysis with the mRNA evidence such as ESTs to identify the novel alternatively spliced variants. We also carried out an extensive analysis of pseudogenes among the PTP family members. We discovered a novel isoform of PTPN18 based on analysis of expressed sequence tags (ESTs) and many splice variants for other PTP members. These results were experimentally validated using experimental techniques such as RT-PCR and Northern blots. A unique, user-friendly web-based resource, 'Protein Tyrosine Phosphatase Resource (PTPR)', that consolidates the gene and protein annotations for all human protein tyrosine phosphatases has been developed and made publicly available.