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📊 RNA-seq & ChIP-seq visualization
- This page allows you to visualize and explore genomic data in various plot types (genome, RNA-seq, microarrays, ChIP-seq).
- The page consists of a sidebar for selecting data and settings, and a main panel for displaying the plots.
🧭 Tab: Navigation
- Left / Right arrows – shift the genome plot by 10,000 base pairs on the X-axis.
- Zoom in / Zoom out – zoom into or out of the displayed genome region.
- Minimal / Maximum value of plot – manually set the plot axis limits.
- Apply Changes – confirms manual axis changes and must be used to trigger reactivity.
🧬 Tab: Selection
- Select Streptomyces species – switch between S. coelicolor and S. venezuelae.
- Show/hide visualizations – choose which plot types to display (Genome, RNA-seq, Microarray, ChIP-seq).
- Choose gene from list – zoom to the selected gene on the genome.
- RNA-seq Plot Data – choose up to 3 RNA-seq datasets.
- ChIP-seq Plot Data – choose one ChIP-seq dataset.
- Choose comparison for analysis – select type of comparison (e.g., strain, timepoint, conditions).
📊 Tab: Plot settings
- LogFC Filtering – filter plot based on lower/higher log fold change values.
- FDR Filtering – show only data with FDR ≤ 0.05.
⬆️ Tab: Upload data
- Browse… / drag & drop file – upload data file from your computer.
- Is RNA-seq file in app format? (Yes/No) – indicate if the format matches app structure.
- Custom file name – assign a name that will appear in plot selectors.
⬇️ Tab: Plot download
- Download png plot – export plot as a PNG image.
- Resolution and size settings – optionally adjust width, height, and DPI before download.
🧾 Additional: Data tables under plots
- RNAseq on plot – genes visible on the RNA-seq plot.
- RNAseq no filter – full RNA-seq dataset (unfiltered).
- ChIPseq in table – genes shown on the ChIP-seq plot.
- Search: – search bar to filter table contents.
📊 Comparison of data
- This page allows comparing datasets visually via Venn diagrams and heatmaps.
- Similar to the RNA-seq & ChIP-seq page, it consists of a sidebar for inputs and a main panel for plots.
🧬 Tab: Selection
- Venn Diagram Data – choose up to 4 comparisons from RNA-seq or microarray datasets (including user uploads) for the Venn diagram and heatmap.
- Heatmap Gene Name Input – type gene names (comma-separated) to filter and display them in the heatmap, e.g., SCO6276, SCO6277.
🔧 Tab: Venn LogFC option
- Allows setting upper and lower logFC thresholds for Venn diagram filtering.
- Does not affect the Heatmap.
- Only comparisons with logFC outside the set range are shown (default: -1.5 to 1.5).
- FDR is always ≤ 0.05 by default – cannot be changed.
⬇️ Tab: Plot download
- Plot Download Venn – download the Venn diagram as a PNG file.
- Plot Download Heat – download the heatmap as a PNG file.
📌 Plot behavior and logic
- Venn diagram supports max. 4 comparisons – if more are selected, an "UpSet" plot is shown instead.
- Below the Venn diagram, genes from shared or unique subsets are listed in tables.
- These gene lists can be copied into the Heatmap gene input field.
- Heatmap shows only genes from selected comparisons, filtered by FDR ≤ 0.05 and the typed gene list.
- Gray cells in the heatmap indicate missing values for selected genes.
- Clustering: similar genes and comparisons are grouped using dendrograms (left for genes, top for comparisons).
🧬 Gene Inspector
- The Gene Inspector tab is a dashboard-like view dedicated to exploring a single gene in detail.
- It integrates RNA-seq, ChIP-seq, and homology search results, along with genbank/uniprot annotation data for each gene.
- The sidebar provides controls for entering the gene locus (e.g., SCO2950), switching species and adjusting various filters.
📖 Panels and Outputs
- Gene Description – shows annotation data, including locus, product, protein length, UniProt links, and notes.
- Normalized gene expression – line plots of normalized RNA-seq expression across timepoints, when grown in liquid medium, with optional extra genes for comparison.
- ChIP-seq predicted binding sites – visualizes binding events around the selected gene, with adjustable flanking region size and dataset selection.
- RNA-seq results – offers both a expression plot and a data table of differential expression results for the chosen gene.
- 16S RNA tree – displays a 16SRNA phylogenetic tree for representative Actinobacteria species with marked presence of selected gene, with filtering options for score and sequence length, plus a corresponding data table.
⚙️ Sidebar Options
- Gene Input – enter a locus tag manually; toggle between S. coelicolor and S. venezuelae.
- Expression Comparison – add multiple genes to overlay their normalized expression profiles.
- 16S RNA tree options – filter homologues by alignment score, minimum and maximum length.
- RNA-seq plot options – filter results by log fold change threshold.
- ChIP-seq plot options – adjust flanking region size and select which ChIP-seq datasets to display.