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...
Cluster analysis and GO enrichment analysis were used to explore the differential expressed TFs. As shown in Fig.5, two distinct clusters were observed when the later stage compared with the previous stage, indicating significant differences in the regulation of transcription factor expression. Therefore...
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...
FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27:1017–8. Article CAS Google Scholar Bruse N, van Heeringen SJ. GrimmeMotifs: an analysis framework for transcription factor motif analysis. bioRxiv. 2018. http://dx.doi.org/10.1101/474403. Tian F, Yang D-C, Meng...
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。
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 ...
Moreover, the conserved motif and gene structure analysis shown that the members of the CeqMYB s were divided into the same subgroups with mostly similar gene structures. In addition, many conserved amino acids in the R2 and R3 domains of CeqMYB s by WebLogo analysis, especially tryptophan ...
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。
Genome-wide identification, classification and analysis of heat shock transcription factor family in maize. BMC Genomics. 2011;12:1–14. Google Scholar Haider S, Rehman S, Ahmad Y, Raza A, Tabassum J, Javed T, Osman HS, Mahmood T. In silico characterization and expression profiles of heat...
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...