CellRegulomiX Interface Help

Run, Score and Network Files

Name of the Run

Purpose
The Run Name is a short textual identifier for your analysis. It is used to:

  • name the output directory;
  • group results under a unique identifier;
  • avoid overwriting previous runs.

Requirements

  • Should be unique if you want to keep multiple runs.
  • Allowed characters: letters (A-Z, a-z), digits (0-9), dashes (-) and underscores (_).
  • Avoid spaces and special characters to prevent filesystem issues.

Example

MyRun_01
TF_analysis_January
AML_case23

Number of Network Files

Description
Defines how many network files will be uploaded. The UI dynamically creates one upload widget per specified file.

Accepted values

  • Minimum: 1
  • Maximum: 5

Network File Format

Description
A network file defines regulatory interactions between transcription factors (TFs) and target genes. Each row represents a directed interaction: TF → Target.

Accepted formats

  • .csv, .tsv, .txt (comma or tab separated)
  • Accepted delimiters: comma ,, tab \t, semicolon ;

Required columns (recommended)

Column Name Description
TF Name of the transcription factor (source)
Target Name of the regulated gene (destination)
Weight (optional) Interaction score or confidence

Example (TSV)

TF  Target  Weight
TP53    CDKN1A  0.92
STAT3   SOCS3   0.81
MYC CCND2   0.76

Notes

  • Use consistent gene naming across files (HGNC symbols, Ensembl IDs, etc.).
  • If header names differ, adapt them before upload or use the app’s mapping options (if available).
  • Duplicate edges are allowed but may be collapsed during processing.

TF Selection

Preselect TFs using positive/negative data

Description
When enabled, TF selection uses two datasets (positive and negative) to rank TFs via differential evidence.

When to use
Enable when your experiment includes positive vs negative/ control samples.

Node Score File

Format
Two-column table with gene identifier and score value.

Column Description
Gene Gene name
Score Numeric score

TF List File

Description
Optional plain list of TFs to force into the analysis.

Format
One TF name per line, or a single-column CSV with header.

3. Target Gene Color Attributes

Continuous Value File

Description
Used to color nodes using continuous values (e.g., expression, fold change).

Example

Gene Value
TP53 2.1
MYC -0.8
JUN 1.7

Category File

Description
Used to color nodes by category/group (discrete values).

Example

Gene Group
TP53 Group1
MYC Group2
JUN Group1

Advanced Parameters

This section collects advanced parameters. Use these only if you understand their algorithmic impact.

Improvement Rate

Controls how aggressively the algorithm expands candidate subnetworks (numeric, default: 2.0).

Max Subnetwork Depth

Maximum expansion depth (integer).

Min Subnetwork Size

Minimum nodes required for a valid subnetwork (integer).

Number of Random Subnetworks

Number of random subnetworks used for significance assessment.

Minimum Number of TFs

Minimum TFs required in a subnetwork.

Overlap Threshold

Controls redundancy between returned subnetworks (0-1).

Seed Type

Seed selection strategy: TFs only, Targets only, or Both.

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