2026-10-09T21:04:30Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33941767 2026-09-19T08:29:42Z category_24193 category_24202 category_24184 category_24382 item_type_3 month_year_09_2026

DEAR-OWL validation scripts and data Daisuke Tsugama (9977096) Kota Kambara (17862556) Genomics and transcriptomics Statistical and quantitative genetics Bioinformatic methods development Plant cell and molecular biology web browser application RNA-seq transcriptome differential expression analysis differentially expressed genes DESeq2 EdgeR Grass Expression Atlas Motif analysis HOMER <p><strong>Data Organization and File Naming Convention</strong></p><p>To ensure maximum computational reproducibility, all validation scripts, input records, and generated output files are contained within a single flat directory structure. This design allows the workflows to be executed immediately without requiring complex relative directory path configurations. Users can easily identify and utilize the datasets based on the following standardized file naming conventions:</p><p><br></p><ul> <li><strong>Execution & Processing Scripts:</strong> <ul> <li><code>validation_script.txt</code>: The primary shell one-liner script used to automate the sequential processing, file renaming, and tool executions.</li> <li><code>*.py</code>: Python scripts responsible for statistical analysis and generating performance/consensus plots (called internally by the shell script).</li> </ul> </li> <li><strong>DEAR-OWL Output Lists:</strong> <ul> <li><code>uploaded*.csv</code>: The DEG consensus lists containing fold-change values and p-values exported from DEAR-OWL. Files derived from the lightweight engine are explicitly distinguished by the suffix <code>_edgeR-like.csv</code>.</li> </ul> </li> <li><strong>Sequence Data (FASTA):</strong> <ul> <li><code>uploaded*.fa</code>: The 500-bp upstream promoter sequences corresponding to the target DEG lists.</li> </ul> </li> <li><strong>Reference DEG Datasets:</strong> <ul> <li><code>*brushed*.txt</code>: Reference DEG lists previously identified and published in Yoon et al. (2024, <em>Plant Physiol Biochem</em>).</li> <li><code>PRJNA*.txt</code>: Reference DEG lists corresponding to the <em>Cenchrus americanus</em> samples from Qazi et al. (2025, <em>Biosci Biotechnol Biochem</em>), also archived in Tsugama et al. (2024, Figshare).</li> </ul> </li> <li><strong>HOMER Analysis Outputs:</strong> <ul> <li><code>Homer*</code> (Directories/Folders): Output directories containing the definitive motif discovery tables, enrichment scores, and sequence logos generated by the HOMER suite.</li> </ul> </li> <li><strong>Intermediate and Outcome Files:</strong> <ul> <li>Other <code>*.png</code>, <code>*.txt</code>, and miscellaneous formats represent the raw input matrices, mid-stage transformation records, and definitive output results.</li> </ul> </li></ul><p><br></p><p>The specific genetic background, treatment conditions, and sample identifiers (e.g., QM2, VIP1-GFP) are explicitly included in the prefix of each respective filename for clear cross-referencing.</p> 2026-09-19T08:29:42Z Dataset Dataset 10.6084/m9.figshare.33941767.v2 https://figshare.com/articles/dataset/DEAR-OWL_validation_scripts_and_data/33941767 CC BY 4.0