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Publication for PTMap
MiR 190b, the highest up regulated miRNA in ERα positive compared to ERα negative breast tumors, a new biomarker in breast cancers?
[…] ER+ and ER−similar to their miRNA (Table ). Thus CTDSPL, EVL, NFYC, OGFRL1 and CTDSP1 are more expressed in ER+ than in ER− like miR-26a1, miR-342-5p, miR-30a, miR-30c2 and miR-26b respectively, and PTMAP2 is less expressed in ER+ than in ER− like miR-1244. Moreover Spearman’s rank correlation analysis revealed a significant and positive correlation between expression of all host genes and its re […]
Pharmacogenomics of Hypertension: A Genome‐Wide, Placebo‐Controlled Cross‐Over Study, Using Four Classes of Antihypertensive Drugs
[…] d ). Two SNPs on chromosome 13, rs7984003 (P=7.8×10−7) and rs2765115 (P=3.6×10−6) showed suggestive evidence of association when systolic ABP responses of both studies were analyzed. Two pseudogenes (PTMAP and GYG1P2) but no obvious protein‐coding gene candidates are located in the vicinity of rs7984003. Of the protein‐coding genes, SPATA13 coding for spermatogenesis‐associated protein 13 lies clo […]
Evaluation of Proteomic Search Engines for the Analysis of Histone Modifications
[…] wn to be very challenging to analyze using conventional commercially available search methods and often require specific in-house developed software to properly deal with their data sets (e.g., MILP, PTMap, MS-TopDown, and FAVA-based workflow). In this study, we present a method to evaluate database search engines on identifying spectra from histone peptides containing PTMs. In this method, no mod […]
Proteomic characterization of novel histone post translational modifications
[…] ifficult. Algorithms have been designed to specifically map histone modifications and identify novel sites of modification [-]. For unbiased novel PTM type discovery, Chen and colleagues  developed PTMap to explore a wide window of mass shifts in small increments and identify unique modifications. It also decreases false positives by scoring unmatched peaks in the MS/MS spectra .Misidentificat […]
Proteomics in epigenetics: new perspectives for cancer research
[…] has been largely facilitated by recent developments in software that deviate from the conventional approach for unmodified peptide identification based on restricted database searches. For instance, PTMap  utilizes sequence alignment to localize sites of PTMs on target proteins while substantially reducing false-positive identifications based on unmatched peaks. While innovative approaches such […]
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