SCD<i>Finder</i>, a Web-based tool for the identification of putative novel ATM and ATR targets

Cara, Lukas R.; Baitemirova, Medina; Duong, Franklin; Larios‐Sanz, Maia; Ribes-Zamora, Albert

doi:10.1093/bioinformatics/btu551

Cited by 1 publication

(1 citation statement)

References 7 publications

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“…We used SCDFinder 23 to perform static database searches in the human, mouse and zebrafish proteomes, looking for proteins containing at least one SCD within their sequences. The results from each search were later cross-referenced using Homologene and we identified 842 SCD-containing human proteins whose homologs in mice and zebrafish also contain an SCD (see Supplementary Table S1 ).…”

Section: Resultsmentioning

confidence: 99%

The ATM- and ATR-related SCD domain is over-represented in proteins involved in nervous system development

Cara

Baitemirova

Follis

et al. 2016

Sci Rep

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ATM and ATR are cellular kinases with a well-characterized role in the DNA-damage response. Although the complete set of ATM/ATR targets is unknown, they often contain clusters of S/TQ motifs that constitute an SCD domain. In this study, we identified putative ATM/ATR targets that have a conserved SCD domain across vertebrates. Using this approach, we have identified novel putative ATM/ATR targets in pathways known to be under direct control of these kinases. Our analysis has also unveiled significant enrichment of SCD-containing proteins in cellular pathways, such as vesicle trafficking and actin cytoskeleton, where a regulating role for ATM/ATR is either unknown or poorly understood, hinting at a much broader and overarching role for these kinases in the cell. Of particular note is the overrepresentation of conserved SCD-containing proteins involved in pathways related to neural development. This finding suggests that ATM/ATR could be directly involved in controlling this process, which may be linked to the adverse neurological effects observed in patients with mutations in ATM.

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Section: Resultsmentioning

confidence: 99%

The ATM- and ATR-related SCD domain is over-represented in proteins involved in nervous system development

Cara

Baitemirova

Follis

et al. 2016

Sci Rep

View full text Add to dashboard Cite

show abstract

SCDFinder, a Web-based tool for the identification of putative novel ATM and ATR targets

Abstract: The application was developed using Pearl and Python, and is available at the following URL: http://ustbioinfo.webfactional.com/scd/.

Cited by 1 publication

References 7 publications

The ATM- and ATR-related SCD domain is over-represented in proteins involved in nervous system development

The ATM- and ATR-related SCD domain is over-represented in proteins involved in nervous system development

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