AIMC Topic: Transcription Factors

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A GO catalogue of human DNA-binding transcription factors.

Biochimica et biophysica acta. Gene regulatory mechanisms Oct 18, 2021
To control gene transcription, DNA-binding transcription factors recognise specific sequence motifs in gene regulatory regions. A complete and reliable GO annotation of all DNA-binding transcription factors is key to investigating the delicate balanc...
DNA Molecular Sequence Annotation Gene Ontology Transcription Factors Databases, Genetic Humans
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Multi-Scale Capsule Network for Predicting DNA-Protein Binding Sites.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2021
Discovering DNA-protein binding sites, also known as motif discovery, is the foundation for further analysis of transcription factors (TFs). Deep learning algorithms such as convolutional neural networks (CNN) have been introduced to motif discovery ...
Algorithms Deep Learning Sequence Analysis, Protein Transcription Factors Protein Binding Chromatin Immunoprecipitation Sequencing DNA-Binding Proteins Computational Biology Binding Sites
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Predicting TF-DNA Binding Motifs from ChIP-seq Datasets Using the Bag-Based Classifier Combined With a Multi-Fold Learning Scheme.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2021
The rapid development of high-throughput sequencing technology provides unique opportunities for studying of transcription factor binding sites, but also brings new computational challenges. Recently, a series of discriminative motif discovery (DMD) ...
DNA Binding Sites Chromatin Immunoprecipitation Sequencing Computational Biology Transcription Factors Machine Learning Algorithms Humans
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Biologically relevant transfer learning improves transcription factor binding prediction.

Genome biology Sep 27, 2021
BACKGROUND: Deep learning has proven to be a powerful technique for transcription factor (TF) binding prediction but requires large training datasets. Transfer learning can reduce the amount of data required for deep learning, while improving overall...
Machine Learning Transcription Factors Chromatin Immunoprecipitation Sequencing Genome
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Evaluation of deep learning approaches for modeling transcription factor sequence specificity.

Genomics Sep 14, 2021
As a key component of gene regulation, transcription factors (TFs) play an important role in a number of biological processes. To fully understand the underlying mechanism of TF-mediated gene regulation, it is therefore critical to accurately identif...
Transcription Factors DNA Binding Sites Neural Networks, Computer Humans Deep Learning
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HOX cluster and their cofactors showed an altered expression pattern in eutopic and ectopic endometriosis tissues.

Reproductive biology and endocrinology : RB&E Sep 1, 2021
Endometriosis is major gynecological disease that affects over 10% of women worldwide and 30%-50% of these women have pelvic pain, abnormal uterine bleeding and infertility. The cause of endometriosis is unknown and there is no definite cure mainly b...
Transcription Factors Endometrium Endometriosis Gene Regulatory Networks Signal Transduction Genes, Homeobox Gene Ontology Homeodomain Proteins Multigene Family Humans Female Adult Gene Expression Profiling Young Adult
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Gene Ontology representation for transcription factor functions.

Biochimica et biophysica acta. Gene regulatory mechanisms Aug 28, 2021
Transcription plays a central role in defining the identity and functionalities of cells, as well as in their responses to changes in the cellular environment. The Gene Ontology (GO) provides a rigorously defined set of concepts that describe the fun...
Databases, Genetic Gene Expression Regulation Gene Ontology Molecular Sequence Annotation Computational Biology Transcription Factors
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Discovering differential genome sequence activity with interpretable and efficient deep learning.

PLoS computational biology Aug 9, 2021
Discovering sequence features that differentially direct cells to alternate fates is key to understanding both cellular development and the consequences of disease related mutations. We introduce Expected Pattern Effect and Differential Expected Patt...
Humans Genome, Human Transcription Factors Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Neural Networks, Computer Deep Learning
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Deep learning-based prediction of TFBSs in plants.

Trends in plant science Jul 24, 2021
Computational Biology Transcription Factors Deep Learning Binding Sites Protein Binding
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Prioritizing and characterizing functionally relevant genes across human tissues.

PLoS computational biology Jul 16, 2021
Knowledge of genes that are critical to a tissue's function remains difficult to ascertain and presents a major bottleneck toward a mechanistic understanding of genotype-phenotype links. Here, we present the first machine learning model-FUGUE-combini...
Gene Expression Regulation, Developmental Genome, Human Tissue Distribution Genome-Wide Association Study Protein Interaction Maps Gene Regulatory Networks Neoplasms Transcriptome Models, Genetic Transcription Factors Humans Multigene Family Genetic Association Studies Machine Learning Female Computational Biology Software Male
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