Volcano plots showing the relative intensities of the mass features detected in the generated knock-out mutants of <i>Streptomyces coelicolor</i> in comparison with the wild-type.

Similar Items

• DmdR1 PWM threshold setting and identification of novel iron boxes in <i>Streptomyces coelicolor.</i>
  by: Hannah E. Augustijn (10773096)
  Published: (2025)
• Extracted ion chromatograms of DFOB and DFOE related metabolites in the knock-out (Δ) mutants of SCO4048 (<i>desJ</i>), SCO4049 (<i>desG</i>) and SCO40450 (<i>desH</i>) compared to the parent <i>S. coelicolor</i> M145 strain.
  by: Hannah E. Augustijn (10773096)
  Published: (2025)
• Extracted ion chromatograms of DFO-related metabolites in the knock-out (Δ) and complementation (C) mutants of SCO4048 (<i>desJ</i>), SCO4049 (<i>desG</i>) and SCO40450 (<i>desH</i>) compared to the parent <i>S. coelicolor</i> M145 strain.
  by: Hannah E. Augustijn (10773096)
  Published: (2025)
• a, Predicted gene regulatory network of <i>Streptomyces coelicolor</i> based on 17 well-known regulators. Each node in the network represents a (regulatory) gene, and every edge represents a PWM predicted regulatory interaction between nodes. The edges colored in dark gray indicate strong PWM prediction scores, while the lighter gray shades represent weaker interactions. Matches within BGC regions are depicted as triangles. In six regions (black circled), the matches fall within a co-expressed region, highlighting their functional relation to these compounds. b, Representation of the four co-expressed regions, including the locations of their detected TFBSs as colored dots. All predicted TFBSs have been experimentally validated in pre-existing work. The data underlying this figure can be found at https://zenodo.org/records/15106944.
  by: Hannah E. Augustijn (10773096)
  Published: (2025)
• a, Anti-correlation of gene expression between <i>dmdR1</i> and its predicted regulon. Left: Pearson correlation coefficients (PCCs) between <i>dmdR1</i> and all genes with a DmdR1 position weight matrix (PWM) score greater than 15 in their regulatory region. The vertical dashed line marks the refined PWM score threshold of 22.875. The horizontal dotted lines mark PCC = ±0.43, corresponding to an adjusted <i>p</i>-value of 0.05. Right: Target genes immediately downstream of a predicted DmdR1 binding site, ordered by decreasing PWM score. Plus and minus indicate the strand of the target gene. Genes marked with an × did not have significant co-expression with <i>dmdR1</i>. Binding site details are given in S2 Table, and the raw data underlying this figure can be found at https://zenodo.org/records/15106944. b, The putative regulon of DmdR1 in <i>Streptomyces coelicolor</i> M145. White dots indicate predicted DmdR1 bind
  by: Hannah E. Augustijn (10773096)
  Published: (2025)