HypoGScale — Hypospadias GRN & PPI Inference
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Nodes
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Seeds
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Modules
Quick guide: 1) Run Hypospadias Inference → 2) choose layout (Interactive/Static) → 3) adjust labels and legends → 4) export PNG.
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Applies to the next Run Inference.
More permutations give stabler empirical p-values.
Only the top-ranked modules get null statistics.
Click the toolbar chip to jump to the current module-level null summary and see observed score, null mean, z-score, empirical p-value and FDR.
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Seed gene
Modules (click to highlight)
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Parameter robustness (Interactive PPI)
Parameter robustness. Sweep selected PPI threshold, community algorithm, and neighborhood settings against the currently loaded baseline. For speed, the sweep temporarily turns module permutation off and compares module membership / top core-gene overlap across reruns.
Parameter robustness heatmap

Rows are parameter combinations. Columns summarize stability relative to the currently loaded baseline: top-1 module overlap, mean overlap across baseline top modules, and top core-gene overlap.

Module membership stability

Each cell shows best Jaccard overlap between a baseline top module and its closest rerun module under the given parameter combination.

Robustness summary table
Consensus core genes
Consensus top modules
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Gene Regulatory Networks (GRN) ⓘ
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Tooltip metadata priority in GRN interactions: Seed genes file / full input seed table > GRN-derived node defaults > generic fallback values. If a gene is present in the input seed list, hover cards resolve Function, Count, and Seed from that seed table first, then fill any remaining missing fields from the current network view.
Function groups
Seed gene ranking (GRN-based) ⓘ
#GeneScoreCountDirect burdenBest direct seed2-hop burdenDegree
Seed gene ranking (GRN-based) ⓘ
Preset emphasizes damaging mutation burden.
#GeneScoreCountDirect burdenBest direct seed2-hop burdenDegree
Importance index
Expanded GRN (GRN + selected module interactions)
Base network follows the GRN interactions view above, which is derived from the loaded GRN edges file. You can then extend that GRN with important selected-module genes and their supporting GRN/PPI interactions. Tooltip metadata in this Expanded GRN still follows the same seed-first rule: input seed table values for Function, Count, and Seed are used before GRN/PPI fallback values.
1.0 100
Source styles:
Source priority in display: Seed genes file > GRN edges file > PPI-inferred module genes. Tooltip metadata priority follows the same seed-first rule: when a node is also an input seed, Function, Count, and Seed are resolved from the seed table before GRN/PPI fallback values. Multi-source overlap is encoded by border color, while tooltip still shows all matched source memberships.
Selected modules: (none)
Manual genes: (none)
Customize Expanded GRN
Recent edits (latest 5)
Tip: right-click any node in Expanded GRN to remove it from current view.
Customize GRN
Tip: right-click any node in the GRN canvas to remove it from current view.
Permutation status will appear after inference.
Module table
Module score chart
Permutation null histogram ⓘ
Null histogram
Null ECDF
Leave-one-out sensitivity ⓘ
Leave-one-out sensitivity: pick a module, select a bounded set of genes, and rerun targeted leave-one-gene-out analysis to see how module score and empirical p change.
Leave-one-out heatmap
Each run removes one selected input gene, reruns module detection, and matches the closest module by overlap. Keep the candidate set small for large modules like M4.
LOO impact overview
How to read this plot
Sensitivity table ⓘ
Gene contribution table ⓘ
Expanded GRN (core + selected module interactions)
Tooltip metadata priority in this Expanded GRN is also seed-first: input seed table values for Function, Count, and Seed override GRN/PPI fallback values whenever the gene is part of the original seed list.
1.0 100
Selected modules: (none)
Manual genes: (none)
Customize Expanded GRN
Recent edits (latest 5)
Tip: right-click any node in Expanded GRN to remove it from current view.
Filter modules
Gene scores (Network)
Function importance ⓘ
Function chart
Top genes by metric
Gene ranking bootstrap robustness (PPI) ⓘ
Gene ranking robustness landscape
Gene tier distribution
Top stability genes
Supplement note: PPI gene-role labels are heuristic / operational annotations of within-run background-network patterns, not disease subtype classifiers.
Gene role infer ⓘ
Role axes will appear after running the current PPI robustness analysis.
Core gene scores ⓘ
Core function importance ⓘ
0.68 0.18 0.09 0.05 | Preset: Mutation-priority
Core function chart
Top core genes by metric ⓘ

Current Core table and charts include input seeds that are outside the PPI background but present in the Full GRN.

Core ranking bootstrap robustness (core-only) ⓘ
Core ranking robustness landscape
Core tier distribution
Top core stability genes
Supplement note: Profile labels are heuristic / operational annotations of within-run core-gene role patterns, not disease subtype classifiers.
Core gene role infer ⓘ
Role axes will appear after running the current core robustness analysis.