Inference and prioritization of tissue-specific regulons in <i>Arabidopsis</i> and <i>Oryza</i>.

ABSTRACT: A regulon refers to a group of genes regulated by a transcription factor binding to regulatory motifs to achieve specific biological functions. To infer tissue-specific gene regulons in Arabidopsis, we developed a novel pipeline named InferReg. InferReg utilizes a gene expression matrix that includes 3400 Arabidopsis transcriptomes to make initial predictions about the regulatory relationships between transcription factors (TFs) and target genes (TGs) using co-expression patterns. It further improves these anticipated interactions by integrating TF binding site enrichment analysis to eliminate false positives that are only supported by expression data. InferReg further trained a graph convolutional network with 133 transcription factors, supported by ChIP-seq, as positive sam

SUBMITTER: Dai H 

PROVIDER: S-EPMC11399499 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature