Examples

This page gives practical user journeys for common BRIDGE tasks.

Showcase dataset snapshot

If you use the showcase-style database, a common setup is:

Table	Omics type	Rows	Datapoint columns
zebrafish_proteomics_Showcase_1	Proteomics	273	18
zebrafish_phosphoproteomics_Showcase_1	Phosphoproteomics	533	18
zebrafish_rnaseq_Showcase_1	RNA-seq	1000	18

Example 1: RNA-seq single-table exploration

Goal:

• inspect variance structure
• identify significant genes

Steps:

1. Load one RNA-seq table in Loading Data.
2. Open PCA and click compute.
3. Open Volcano Plot, choose contrast, set thresholds, compute.
4. Open Gene Expression and inspect selected genes over datapoints.

Example 2: Proteomics table with enrichment

Goal:

• find significant signals and enriched pathways

Steps:

1. Load one proteomics table.
2. Run DE Heatmap and Volcano Plot.
3. Open Enrichment Analysis.
4. Pick contrast + database (GO, KEGG, or Reactome), set thresholds, compute.

Example 3: Raw integration across datasets

Goal:

• compare trends across omics without significance filtering

Steps:

1. Load two or more datasets.
2. Open Raw Integration.
3. Select tables and matching datapoint columns.
4. Check integration preview.
5. Compute and inspect integrated raw table + datapoints plot.

Example 4: Processed integration across matched contrasts

Goal:

• find intersecting significant IDs across datasets

Steps:

1. Load at least two datasets with computed processed outputs.
2. Open Processed Integration.
3. Select one contrast per dataset.
4. Set p-value/LFC thresholds and cluster number k.
5. Compute and inspect processed tables, heatmaps, and LFC scatterplots.

Tips:

• Use comparable contrasts across datasets.
• Start with moderate thresholds, then refine.
• Check preview dimensions before interpretation.