Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here we present a publicly available, large-scale transcription start site (TSS) dataset in plants using a high-resolution method for analysis of 5’ ends of mRNA transcripts. Our dataset...
Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here we present a publicly available, large-scale transcription start site (TSS) dataset in plants using a high-resolution method for analysis of 5’ ends of mRNA transcripts. Our dataset...
Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated
with physiological ripening stages and the transcriptional changes between stages within the ripening programme.
In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified,
mainly due to the...
Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated
with physiological ripening stages and the transcriptional changes between stages within the ripening programme.
In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified,
mainly due to the...
MOTIVATION: The computational identification of gene transcription start sites (TSSs) can provide insights into the regulation and function of genes without performing expensive experiments, particularly in organisms with incomplete annotations. High-resolution general-purpose TSS prediction remains a challenging problem, with little recent progress on the identification and differentiation of TSSs which...
Background:
Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. While this method was...
Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated
with physiological ripening stages and the transcriptional changes between stages within the ripening programme.
In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified,
mainly due to the...
Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here we present a publicly available, large-scale transcription start site (TSS) dataset in plants using a high-resolution method for analysis of 5’ ends of mRNA transcripts. Our dataset...
WaRSwap is a randomization algorithm that for the first time provides a practical network motif discovery method for large multi-layer networks, for example those that include transcription factors, microRNAs, and non-regulatory protein coding genes. The algorithm is applicable to systems with tens of thousands of genes, while accounting for critical...
