In order to show Pyicos applicability to CLIP-Seq experiments, we reproduced the results from Xue et al. (2009), where the interacting RNA sites for the polypyrimidine tract binding protein were mapped to the reference human genome.
Subsequently three different fragments from the M antigen structure were generated and the binding of a series of mAbs produced using the whole protein were mapped.
The DNA-binding domain for M. tuberculosis RelBE proteins was mapped using several short duplex DNA substrates, designated as p5, p3, and p7.
In this study, 53BP1 binding protein was probed to map the DNA DSBs damage.
Fatty acid binding protein 6 (FABP6), which was mapped to chromosome 16 in 2007 [ 62], was also found to be significant in the Duroc population in this study.
In addition, expression patterns of genes that encoded cytochrome P450, zinc finger protein, MYB domain protein, and WRKY DNA-binding protein that were mapped here were changed in SCN induced soybean roots [ 65– 65].
LTP1, identified as a gene encoding calmodulin-binding protein [ 75], was mapped on the QRn5 locus.
The HECTD3 protein domain responsible for caspase-8 binding was mapped.
RIZ, retinoblastoma protein (Rb -interacting zinc-fingeRb -interacting was isolated during functional screening for Rb-binding proteins (Buyse et al, 1995) and was mapped to 1p36.2; the RIZ locus is a target of frequent deletion in hepatocellular carcinoma (Fang et al, 2000).
To restrict protein annotations to DNA-binding domains, each protein domain is mapped to its respective GO-annotation in Pfam and only considered when classified as 'DNA-binding'.
