[HTML][HTML] Building transcription factor binding site models to understand gene regulation in plants

X Lai, A Stigliani, G Vachon, C Carles, C Smaczniak… - Molecular plant, 2019 - cell.com
Transcription factors (TFs) are key cellular components that control gene expression. They
recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to …

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

J Jin, F Tian, DC Yang, YQ Meng, L Kong… - Nucleic acids …, 2016 - academic.oup.com
With the goal of providing a comprehensive, high-quality resource for both plant transcription
factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF …

Elucidating the biology of transcription factor–DNA interaction for accurate identification of cis-regulatory elements

M Hajheidari, SC Huang - Current opinion in plant biology, 2022 - Elsevier
Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating
developmental and environmental signals through binding to specific cis-regulatory …

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

I Rauluseviciute, R Riudavets-Puig… - Nucleic Acids …, 2024 - academic.oup.com
Abstract JASPAR (https://jaspar. elixir. no/) is a widely-used open-access database
presenting manually curated high-quality and non-redundant DNA-binding profiles for …

Exploiting genomic features to improve the prediction of transcription factor-binding sites in plants

Q Rivière, M Corso, M Ciortan, G Noël… - Plant and Cell …, 2022 - academic.oup.com
The identification of transcription factor (TF) target genes is central in biology. A popular
approach is based on the location by pattern matching of potential cis-regulatory elements …

Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors

CP Yu, SCC Chen, YM Chang… - Proceedings of the …, 2015 - National Acad Sciences
Maize is a major crop and a model plant for studying C4 photosynthesis and leaf
development. However, a genomewide regulatory network of leaf development is not yet …

PlantRegMap: charting functional regulatory maps in plants

F Tian, DC Yang, YQ Meng, J Jin… - Nucleic acids research, 2020 - academic.oup.com
With the goal of charting plant transcriptional regulatory maps (ie transcription factors (TFs),
cis-elements and interactions between them), we have upgraded the TF-centred database …

[HTML][HTML] Base-resolution prediction of transcription factor binding signals by a deep learning framework

Q Zhang, Y He, S Wang, Z Chen, Z Guo… - PLoS computational …, 2022 - journals.plos.org
Transcription factors (TFs) play an important role in regulating gene expression, thus the
identification of the sites bound by them has become a fundamental step for molecular and …

DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape

P Ding, Y Wang, X Zhang, X Gao, G Liu… - Briefings in …, 2023 - academic.oup.com
Precise targeting of transcription factor binding sites (TFBSs) is essential to comprehending
transcriptional regulatory processes and investigating cellular function. Although several …

[HTML][HTML] Positional distribution of transcription factor binding sites in Arabidopsis thaliana

CP Yu, JJ Lin, WH Li - Scientific reports, 2016 - nature.com
Binding of a transcription factor (TF) to its DNA binding sites (TFBSs) is a critical step to
initiate the transcription of its target genes. It is therefore interesting to know where the …