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. 2017 Aug 28;5:48. doi: 10.3389/fbioe.2017.00048

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Copyright © 2017 Roy, Yun, Madahian, Berry, Deng, Goldowitz and Homayouni.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Screen shot of TREMEL (Transcription REgulatory Modules Extracted from Literature) tool. (A) Search feature allows the user to query genes, TFs, or terms across all 2,861 ATMs. In addition, complex queries involving a combination of any of the three entities can be performed by adding another query box. (B) Overview display shows all of the ATMs which relate to the query with respect to the rank of the query entity, k, and ATM number. (C) Displays the ranked genes, TFs, and terms for the selected ATM in panel (B). In addition, the enriched GO and KEGG categories are displayed in order for the user to quickly compare the NTF terms against human curation.