A sequence motif is a short recurring pattern with biological significance such as a DNA-recognition sequence for a transcription factor (TF), an mRNA splicing signal, or a functional region of a protein domain. Many high-throughput experimental approaches and computational tools have been developed...
Detecting changes in the activity of a transcription factor (TF) in response to a perturbation provides insights into the underlying cellular process. Transcription Factor Enrichment Analysis (TFEA) is a robust and reliable computational method that detects positional motif enrichment associated with change...
本文提介绍了scFAN(single-cell factor analysis network单细胞因子分析网络),这是一种深度学习模型,可以预测单个细胞中全基因组的转录因子结合网络。 scFAN包括对大量的数据进行“预训练模型”训练,然后使用DNA序列数据,汇总的相似scATAC-seq数据和可定位性数据的组合,将其用于预测单细胞水平上的转录因子结合。 scFAN...
Recently, several groups have reported that proteins containing a short VQ (FxxxVQxLTG) motif interact with WRKY proteins. We have recently discovered that two VQ proteins from Arabidopsis (Arabidopsis thaliana), SIGMA FACTOR-INTERACTING PROTEIN1 and SIGMA FACTOR-INTERACTING PROTEIN2, act as ...
研究可以做得很浅,查查genecard数据库,从数据库里找找motif,用工具跑跑target gene,构建一下基因调控网络GRN。 研究也可以做得很深,了解一个物种里面有哪些transcription factor families,这些转录因子各自是如何发挥作用的,这些家族是如何归类的,各自有什么特性。
Motif analysis was done using the MEME suite software package with default parameters [26]. Meme-chip was used for de-novo motif prediction, AME for motif enrichment analysis, Fimo for mapping motifs to DNA sequences, and TOMTOM for motif comparisons. Soybean transcription factor (TF) motif po...
Interestingly, a genome-wide analysis revealed that in addition to CTCF also the YY1 DNA-binding factor was enriched at human chromatin insulators [59]. YY1 has the ability to bind both DNA and RNA [47], raising the possibility that RNAs are also involved in the association of YY1 at ...
Gene structure analysis showed that the number of introns varied from 0 to 12. Motif analysis revealed that all of the identified AcNACs had the conserved NAC domain and motif 6 is the conserved motif. Most of the AcNACs were located in chromosome except AcNAC68, AcNAC70, AcNAC71 and ...
For each potential TFBSiin the genome, its binding status is a hidden variable, either bound (bi = 1) or unbound (bi = 0). To estimate the binding probability, we hypothesized that a motif is more likely to be functional and bound by the factor, if it is closer to a tran...
motif that can be attributed to the Dux factor, we used a previously published ChIP-seq for Dux19. The genome was scanned for binding sites, followed by binding site enrichment analysis of ChIP-peaks against the whole genome. We found the highest enrichment for motif 20, which is a motif ...