There was no low-throughput site information in HPRD.
Currently, PSP spans 50,636 proteins, 1,933,888 MS peptides, 438,576 high-throughput MS sites, 20,262 low-throughput sites, and 18,374 curated papers.
Our text mining efforts captured 11 of the 12 low-throughput sites (92%); in addition, we uncovered one site (Thr-608) that only had high-throughput evidence in the phosphorylation databases.
Sassetti and co-workers performed a high throughput Transposon Site Hybridisation Mutagenesis study to identify essential genes in M. tuberculosis while Raman and co-workers performed a flux balance analysis of the mycolic acid pathway in M. tuberculosis, followed by in silico gene deletions to identify essential genes/putative drug targets.
An excellent case study for coordinating operational and data quality-control workflows for a high-throughput multi-site embryo expression analysis has been demonstrated by the EUREXPRESS project (Diez-Roux et al., 2011).
Several variations of high throughput transposon insertion site sequencing have been reported, including transposon directed insertion-site sequencing (TraDIS), insertion sequencing (INSeq), high-throughput insertion tracking by deep sequencing (HITS), and transposon sequencing (Tn-Seq) [ 22- 25].
Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs.
Using a high-throughput PCR-based site specific chromatin condensation assay, we identified a compound that reactivated Cyclin-Dependent Kinase Inhibitor 2A (CDKN2A) in myeloma cells and suppressed expression of DNMT1 from a library of 5120 chemically diverse small molecules.
Protein phosphorylation can occur on multiple distinct sites throughput the given protein [ 33, 34].
High-throughput L1 integration site sequencing has since revealed 9 and 69 de novo L1 insertions, respectively, in lung and colorectal tumors (Iskow et al., 2010; Solyom et al., 2012), whereas cancer genome resequencing elucidated a further 183 tumor-specific L1 insertions in colorectal, ovarian, and prostate cancer (Lee et al., 2012).
Moreover, we identified low-throughput evidence for Thr-608 phosphorylation of BUB1B, whereas the phosphorylation databases had only high-throughput evidence for this site.
