Novel data fusion method and exploration of multiple information sources for transcription factor target gene prediction

dc.contributorAalto-yliopistofi
dc.contributorAalto Universityen
dc.contributor.authorDai, Xiaofeng
dc.contributor.authorLähdesmäki, Harri
dc.date.accessioned2017-05-30T12:19:02Z
dc.date.available2017-05-30T12:19:02Z
dc.date.issued2010
dc.description.abstractBackground: Revealing protein-DNA interactions is a key problem in understanding transcriptional regulation at mechanistic level. Computational methods have an important role in predicting transcription factor target gene genomewide. Multiple data fusion provides a natural way to improve transcription factor target gene predictions because sequence specificities alone are not sufficient to accurately predict transcription factor binding sites. Methods: Here we develop a new data fusion method to combine multiple genome-level data sources and study the extent to which DNA duplex stability and nucleosome positioning information, either alone or in combination with other data sources, can improve the prediction of transcription factor target gene. Results. Results on a carefully constructed test set of verified binding sites in mouse genome demonstrate that our new multiple data fusion method can reduce false positive rates, and that DNA duplex stability and nucleosome occupation data can improve the accuracy oftranscription factor target gene predictions, especially when combined with other genome-level data sources. Cross-validation and other randomization tests confirm the predictive performance of our method. Our results also show that nonredundant data sources provide the most efficient data fusion.en
dc.description.versionPeer revieweden
dc.format.extent1-15
dc.format.mimetypeapplication/pdf
dc.identifier.citationDai , X & Lähdesmäki , H 2010 , ' Novel data fusion method and exploration of multiple information sources for transcription factor target gene prediction ' , Eurasip Journal on Advances in Signal Processing , vol. 2010 , 235795 , pp. 1-15 . https://doi.org/10.1155/2010/235795en
dc.identifier.doi10.1155/2010/235795
dc.identifier.issn1687-6172
dc.identifier.issn1687-6180
dc.identifier.otherPURE UUID: 63fcc229-57fd-4d97-9994-7b85fafe0b2c
dc.identifier.otherPURE ITEMURL: https://research.aalto.fi/en/publications/63fcc229-57fd-4d97-9994-7b85fafe0b2c
dc.identifier.otherPURE FILEURL: https://research.aalto.fi/files/13004431/art_10.1155_2010_235795.pdf
dc.identifier.urihttps://aaltodoc.aalto.fi/handle/123456789/26466
dc.identifier.urnURN:NBN:fi:aalto-201705305081
dc.language.isoenen
dc.relation.ispartofseriesEURASIP JOURNAL ON ADVANCES IN SIGNAL PROCESSINGen
dc.relation.ispartofseriesVolume 2010en
dc.rightsopenAccessen
dc.titleNovel data fusion method and exploration of multiple information sources for transcription factor target gene predictionen
dc.typeA1 Alkuperäisartikkeli tieteellisessä aikakauslehdessäfi
dc.type.versionpublishedVersion
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