The biological screening equivalent of the statistical Biological datasets are becoming

The biological screening equivalent of the statistical Biological datasets are becoming ever more complex so it is of chain rule (or general product rule) of probability: it places less vital importance to enable quick and intuitive access. We thereemphasis on hits from any individual screen and instead focuses fore put great emphasis on an interactive database, named bioprimarily on factors and pathways that score in several screens. LOGIC (http://www.biologic-db.org), which makes it straightforIts primary aim is to discover new pathways/factors, and the ward to retrieve data on any individual human gene or protein,Relative expression1606 Cell Reports 15, 1597?610, May 17,Surviving fractionwhether it has scored in our screens or not (“bioLOGIC Data”). Importantly, bioLOGIC allows one-click access to basic information about individual candidates in different public databases, as well as immediate access to information about the protein’s functional JNJ-26481585 web domains and about the protein complexes it belongs to. It is possible, for example, to directly learn how other subunits of the same complex score in the screens (“Category members”). Finally, bioLOGIC “Categoryview” makes it possible to quickly sample, for example, how all proteins within a particular gene ontology category scored in the screens. The bioLOGIC interface thus permits quick judgment of the relevance and importance in the DNA damage response of any protein or process of interest. Pathways, Processes, and Complexes At the systems level, the multiomic approach and bioLOGIC provide a birds-eye view of the cellular responses triggered by UV irradiation. As expected, DNA/chromatin- and RNA-related processes dominate the list, including processes such as mRNA splicing, RNAPII transcript elongation, chromosome maintenance, and DNA repair, and protein complexes such as Spliceosome, PAF complex, and MeCP1, for example. A multi-level overlap between genome instability and mRNA splicing has become apparent over the last few years (Lenzken et al., 2013; Chan et al., 2014), and this connection is obvious in our data as well. Interestingly, our data also corroborate anecdotal evidence for an overlap between the response to UV irradiation and double-strand DNA breaks. This overlap might be based on a re-use of response proteins and signaling pathways for different kinds of DNA damage. However, it is equally possible that transcription-impeding damage caused by UV irradiation results in double-strand breaks more frequently than previously assumed, for example through the formation of R loops and their WP1066 clinical trials faulty processing, as suggested by Sollier and Cimprich (2015). Finally, it is not impossible that the doses of UV irradiation used in our study are high enough to directly cause some double-strand breaks or inter-strand DNA crosslinks, which could also help explain some of the observations. It is worth noting that DNA damage response pathways, such as the ATM pathway, can also be activated by replication stress, which occurs as a consequence of UV-induced DNA damage at later time points (Zeman and Cimprich, 2014). Although we believe that replication stress is not a major factor in our results, a follow-up study specifically targeted at this pathway would be required to tease apart the responses to DNA damage and replication stress. Besides the systems level overlaps described above, unexpected connections were also uncovered. The high scores of ribosomal subunits is a particularly strikin.The biological screening equivalent of the statistical Biological datasets are becoming ever more complex so it is of chain rule (or general product rule) of probability: it places less vital importance to enable quick and intuitive access. We thereemphasis on hits from any individual screen and instead focuses fore put great emphasis on an interactive database, named bioprimarily on factors and pathways that score in several screens. LOGIC (http://www.biologic-db.org), which makes it straightforIts primary aim is to discover new pathways/factors, and the ward to retrieve data on any individual human gene or protein,Relative expression1606 Cell Reports 15, 1597?610, May 17,Surviving fractionwhether it has scored in our screens or not (“bioLOGIC Data”). Importantly, bioLOGIC allows one-click access to basic information about individual candidates in different public databases, as well as immediate access to information about the protein’s functional domains and about the protein complexes it belongs to. It is possible, for example, to directly learn how other subunits of the same complex score in the screens (“Category members”). Finally, bioLOGIC “Categoryview” makes it possible to quickly sample, for example, how all proteins within a particular gene ontology category scored in the screens. The bioLOGIC interface thus permits quick judgment of the relevance and importance in the DNA damage response of any protein or process of interest. Pathways, Processes, and Complexes At the systems level, the multiomic approach and bioLOGIC provide a birds-eye view of the cellular responses triggered by UV irradiation. As expected, DNA/chromatin- and RNA-related processes dominate the list, including processes such as mRNA splicing, RNAPII transcript elongation, chromosome maintenance, and DNA repair, and protein complexes such as Spliceosome, PAF complex, and MeCP1, for example. A multi-level overlap between genome instability and mRNA splicing has become apparent over the last few years (Lenzken et al., 2013; Chan et al., 2014), and this connection is obvious in our data as well. Interestingly, our data also corroborate anecdotal evidence for an overlap between the response to UV irradiation and double-strand DNA breaks. This overlap might be based on a re-use of response proteins and signaling pathways for different kinds of DNA damage. However, it is equally possible that transcription-impeding damage caused by UV irradiation results in double-strand breaks more frequently than previously assumed, for example through the formation of R loops and their faulty processing, as suggested by Sollier and Cimprich (2015). Finally, it is not impossible that the doses of UV irradiation used in our study are high enough to directly cause some double-strand breaks or inter-strand DNA crosslinks, which could also help explain some of the observations. It is worth noting that DNA damage response pathways, such as the ATM pathway, can also be activated by replication stress, which occurs as a consequence of UV-induced DNA damage at later time points (Zeman and Cimprich, 2014). Although we believe that replication stress is not a major factor in our results, a follow-up study specifically targeted at this pathway would be required to tease apart the responses to DNA damage and replication stress. Besides the systems level overlaps described above, unexpected connections were also uncovered. The high scores of ribosomal subunits is a particularly strikin.