In this paper, we present TransPrise鈥攁n efficient deep learning tool for predicting positions of eukaryotic transcription start sites. TransPrise offers significant improvement over existing promoter-prediction methods. To illustrate this, we compared predictions of TransPrise with the TSSPlant ...
Genes are transcribed from transcription start sites (TSSs), and their position in a genome is strictly controlled to avoid mis-expression of undesired regions. In this study, we designed and developed a methodology for the evaluation of promoter context
The core promoter determines the start site of transcription, controls the direction of transcription and directs the assembly of the preinitiation complex (PIC). The PIC is comprised of two groups of factors: (a) General transcription factors including RNA polymerase II, TFIIA, TFIIB, TFIID, ...
we assessed the TEFM protein stability in patient-derived primary skin fibroblasts. The steady-state level of TEFM was substantially reduced in P2 and P3 fibroblasts as compared to the controls, consistent with our prediction of p.(Pro157Ala) (P2) and p.(Ile159Lys) (P3) impacting protein co...
Prediction of TF targets As mentioned above, the combination of RPs defined by ChIP-seq peaks and DGE analysis improves the inference of direct TF target genes in the model species [13]. However, a general and user-friendly tool for the less well-studied species is currently not available. ...
(-24/-12 for σ54, -35/-10 for all others; Methods). For prediction of σE1and σE9promoters, we used a different approach. These two σ factors belong to the ECF class of σ factors, which are often autoregulatory on their own operons [66]. We had previously shown that ...
Here, we present INFLAMeR, an ML-based tool for the classification and prediction of functional lncRNAs. INFLAMeR uses both constant and variable genomic features that allow for the prediction of functional lncRNAs in a cell type-specific manner. The variability in lncRNA expression between cell ...
The targeted sequences in DNA, calledcis-actingsequences, include promoters, such asTATA boxes, CAT, GC, and others, generally located upstream the start site of the coding portion of the gene. These sequences are targeted, among others, by theTATA box binding proteinand a series of transc...
Non-template to template expression difference is shown as a function of distance from the transcription start site (TSS). b, Expression of PPARA, FOXA1 and REST TFBSs in the template and non-template orientation as a function of distance from TSS, for n = 2 background sequences. ...
Bacterial σI factors of the σ70-family are widespread in Bacilli and Clostridia and are involved in the heat shock response, iron metabolism, virulence, and carbohydrate sensing. A multiplicity of σI paralogues in some cellulolytic bacteria have been