FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W1971906694> ?p ?o ?g. }

• W1971906694 endingPage "e49086" @default.
• W1971906694 startingPage "e49086" @default.
• W1971906694 abstract "To know the map between transcription factors (TFs) and their binding sites is essential to reverse engineer the regulation process. Only about 10%–20% of the transcription factor binding motifs (TFBMs) have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory “DNA words.” From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%—far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of “DNA words,” newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters." @default.
• W1971906694 created "2016-06-24" @default.
• W1971906694 creator A5048193070 @default.
• W1971906694 creator A5071542199 @default.
• W1971906694 creator A5078962332 @default.
• W1971906694 date "2012-11-28" @default.
• W1971906694 modified "2023-10-16" @default.
• W1971906694 title "Comprehensive Human Transcription Factor Binding Site Map for Combinatory Binding Motifs Discovery" @default.
• W1971906694 cites W1498410508 @default.
• W1971906694 cites W1501572782 @default.
• W1971906694 cites W1609557900 @default.
• W1971906694 cites W1968653474 @default.
• W1971906694 cites W1969676330 @default.
• W1971906694 cites W1974365957 @default.
• W1971906694 cites W1975924111 @default.
• W1971906694 cites W1979119703 @default.
• W1971906694 cites W1984053739 @default.
• W1971906694 cites W1992000554 @default.
• W1971906694 cites W1997889534 @default.
• W1971906694 cites W2035934212 @default.
• W1971906694 cites W2036131961 @default.
• W1971906694 cites W2038044292 @default.
• W1971906694 cites W2039561007 @default.
• W1971906694 cites W2042392223 @default.
• W1971906694 cites W2045385554 @default.
• W1971906694 cites W2054624670 @default.
• W1971906694 cites W2055575272 @default.
• W1971906694 cites W2084908610 @default.
• W1971906694 cites W2085442947 @default.
• W1971906694 cites W2087064593 @default.
• W1971906694 cites W2088514277 @default.
• W1971906694 cites W2090037139 @default.
• W1971906694 cites W2095718954 @default.
• W1971906694 cites W2098412979 @default.
• W1971906694 cites W2099812803 @default.
• W1971906694 cites W2103017472 @default.
• W1971906694 cites W2103914320 @default.
• W1971906694 cites W2106963468 @default.
• W1971906694 cites W2107283089 @default.
• W1971906694 cites W2107575419 @default.
• W1971906694 cites W2108241558 @default.
• W1971906694 cites W2112717966 @default.
• W1971906694 cites W2115761267 @default.
• W1971906694 cites W2117139889 @default.
• W1971906694 cites W2118290853 @default.
• W1971906694 cites W2118533197 @default.
• W1971906694 cites W2119754217 @default.
• W1971906694 cites W2123292855 @default.
• W1971906694 cites W2127297032 @default.
• W1971906694 cites W2131386482 @default.
• W1971906694 cites W2131706188 @default.
• W1971906694 cites W2135030836 @default.
• W1971906694 cites W2136145671 @default.
• W1971906694 cites W2138977668 @default.
• W1971906694 cites W2140754446 @default.
• W1971906694 cites W2142046859 @default.
• W1971906694 cites W2145091349 @default.
• W1971906694 cites W2149769193 @default.
• W1971906694 cites W2161920802 @default.
• W1971906694 cites W2162165765 @default.
• W1971906694 cites W2164814636 @default.
• W1971906694 cites W2167713786 @default.
• W1971906694 cites W2168168636 @default.
• W1971906694 cites W2342083870 @default.
• W1971906694 cites W2610493035 @default.
• W1971906694 cites W299839057 @default.
• W1971906694 cites W4300958603 @default.
• W1971906694 cites W4954057 @default.
• W1971906694 cites W938539187 @default.
• W1971906694 cites W953729042 @default.
• W1971906694 cites W2033966998 @default.
• W1971906694 doi "https://doi.org/10.1371/journal.pone.0049086" @default.
• W1971906694 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3509107" @default.
• W1971906694 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/23209563" @default.
• W1971906694 hasPublicationYear "2012" @default.
• W1971906694 type Work @default.
• W1971906694 sameAs 1971906694 @default.
• W1971906694 citedByCount "6" @default.
• W1971906694 countsByYear W19719066942013 @default.
• W1971906694 countsByYear W19719066942014 @default.
• W1971906694 countsByYear W19719066942016 @default.
• W1971906694 countsByYear W19719066942017 @default.
• W1971906694 countsByYear W19719066942020 @default.
• W1971906694 countsByYear W19719066942022 @default.
• W1971906694 crossrefType "journal-article" @default.
• W1971906694 hasAuthorship W1971906694A5048193070 @default.
• W1971906694 hasAuthorship W1971906694A5071542199 @default.
• W1971906694 hasAuthorship W1971906694A5078962332 @default.
• W1971906694 hasBestOaLocation W19719066941 @default.
• W1971906694 hasConcept C101762097 @default.
• W1971906694 hasConcept C104317684 @default.
• W1971906694 hasConcept C107824862 @default.
• W1971906694 hasConcept C111936080 @default.
• W1971906694 hasConcept C150194340 @default.
• W1971906694 hasConcept C190796033 @default.
• W1971906694 hasConcept C3662595 @default.
• W1971906694 hasConcept C54355233 @default.
• W1971906694 hasConcept C70721500 @default.

• next