spred 0.1.1

Splicing-regulatory Driver Genes Identification Tool

SpReD-GIT

Splicing-regulatory Driver Genes Identification Tool

SpReD-GIT is a computational tool for identifying splicing-regulatory driver genes (SDGs) based on isoform-level expression quantification, such as outputs from XAEM or RSEM.

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Prerequisites

Python >= 3.7 (Python 3.8 recommended)

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Installation

Recommended installation using Conda:

conda create -n SpReD python==3.8
conda activate SpReD
pip install spred

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Input Files

1. Count Matrix File (matrix.count.input.tsv)

transcript_id	Case1	Case2	Case3	Control1	Control2	Control3
ENST00000513924.2	153	130	90	78	158	110
ENST00000511178.1	12	36	12	17	12	10
ENST00000524846.5	224	470	195	275	380	612
ENST00000294428.8	4	61	1	28	23	35
ENST00000371072.8	240	281	229	339	282	291
ENST00000418058.1	7	17	0	19	13	4
ENST00000367006.8	154	181	127	142	246	188
ENST00000419091.7	67	125	61	11	12	67
ENST00000452621.6	42	59	52	95	59	84

• Rows: Transcript-level identifiers (e.g., Ensembl IDs)
• Columns: Sample names (must match group file)

2. Group File (group.tsv)

Sample	Group
Case1	Case
Case2	Case
Case3	Case
Control1	Control
Control2	Control
Control3	Control

• Sample: Must match column names in the count matrix
• Group: Define condition labels (e.g., Case vs Control)

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Quick Start

1. Run the full pipeline including analysis, enrichment, and visualization:

spred run-all -m matrix.count.input.tsv -e group.tsv -g Group -c1 Case -c2 Control -o outdir --species human

2. Run the differential analysis module (analyze)

This module performs the following comparisons between Case and Control groups:

• DGE: Differentially Expressed Genes
• DTE: Differential Transcript Expression
• SDG: Splicing-regulatory Driver Genes

spred analyze -m matrix.count.input.tsv -e group.tsv -g Group -c1 Case -c2 Control -o outdir --species human

3. Run functional enrichment analysis (enrich)

Performs GO/KEGG enrichment analysis on results from DGE, DTE, or SDG. Supports multiple correction methods

spred enrich -i outdir/results/tables/Case_vs_Control.gene.deg.results.tsv --protein-coding --multitest hs
spred enrich -i outdir/results/tables/Case_vs_Control.isoform.dte.results.tsv --protein-coding --multitest hs
spred enrich -i outdir/results/tables/Case_vs_Control.sdGenes.results.tsv --protein-coding --multitest fdr_bh

4. Generate volcano plots (for DGE and DTE results) plot-volcano

spred plot-volcano -i outdir/results/tables/kogo/Case_vs_Control.gene.deg.results.for_kogo.table.tsv --filter-lfc 1
spred plot-volcano -i outdir/results/tables/kogo/Case_vs_Control.isoform.dte.results.for_kogo.table.tsv --filter-lfc 1

5. Generate Mahalanobis plots (for SDG results) plot-manhan

spred plot-manhan -i outdir/results/tables/kogo/Case_vs_Control.sdGenes.results.for_kogo.table.tsv

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Definitions

• DGE (Differentially Expressed Genes): Genes that show statistically significant expression changes between groups.
• DTE (Differential Transcript Expression): Transcript-level expression differences, potentially indicating alternative splicing events.
• SDG (Splicing-regulatory Driver Genes): Genes that exhibit splicing regulatory alterations, potentially playing a key role in disease mechanisms.

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Output Structure

outdir/
└── results/
    ├── kogo/
    │   ├── Case_vs_Control.gene.deg.for_kogo.genelist.tsv
    │   ├── Case_vs_Control.gene.deg.for_kogo.table.tsv
    │   ├── Case_vs_Control.gene.deg.kogo.barplot.pdf
    │   ├── Case_vs_Control.gene.deg.kogo.barplot.png
    │   ├── Case_vs_Control.gene.deg.kogo.results.tsv
    │   ├── Case_vs_Control.isoform.dtg.for_kogo.genelist.tsv
    │   ├── Case_vs_Control.isoform.dtg.for_kogo.table.tsv
    │   ├── Case_vs_Control.isoform.dtg.kogo.barplot.pdf
    │   ├── Case_vs_Control.isoform.dtg.kogo.barplot.png
    │   ├── Case_vs_Control.isoform.dtg.kogo.results.tsv
    │   ├── Case_vs_Control.sdGenes.deg.for_kogo.genelist.tsv
    │   ├── Case_vs_Control.sdGenes.deg.for_kogo.table.tsv
    │   ├── Case_vs_Control.sdGenes.deg.kogo.barplot.pdf
    │   ├── Case_vs_Control.sdGenes.deg.kogo.barplot.png
    │   ├── Case_vs_Control.sdGenes.deg.kogo.results.tsv
    │   └── tables/
    │       ├── Case_vs_Control.GO_BP.results.all.xls
    │       └── Case_vs_Control.KEGG.results.all.xls
    │
    └── tables/
        ├── Case_vs_Control.gene.deg.for_kogo.table.tsv
        ├── Case_vs_Control.gene.deg.for_kogo.volcano.pdf
        ├── Case_vs_Control.gene.deg.for_kogo.volcano.png
        ├── Case_vs_Control.gene.deg.results.tsv
        ├── Case_vs_Control.isoform.dtg.for_kogo.table.tsv
        ├── Case_vs_Control.isoform.dtg.for_kogo.volcano.pdf
        ├── Case_vs_Control.isoform.dtg.for_kogo.volcano.png
        ├── Case_vs_Control.isoform.dtg.results.tsv
        ├── Case_vs_Control.sdGenes.deg.for_kogo.manha.pdf
        ├── Case_vs_Control.sdGenes.deg.for_kogo.manha.png
        ├── Case_vs_Control.sdGenes.deg.for_kogo.table.tsv
        ├── Case_vs_Control.sdGenes.results.tsv

Description

• kogo/: Contains all enrichment input and output related to KOGO (GO/KEGG) analysis.

  • *.genelist.tsv: Gene list used for enrichment.
  • *.table.tsv: Formatted input tables.
  • *.kogo.barplot.*: Bar plots of enrichment results (PDF and PNG).
  • *.kogo.results.tsv: Raw enrichment result tables.
  • tables/: Final GO/KEGG enrichment outputs.

• tables/: Differential expression and splicing results.

  • *.results.tsv: Full statistical test results.
  • *.volcano.*: Volcano plots for gene/isoform level results.
  • *.manha.*: Mahalanobis plots for SDG analysis.
  • *.for_kogo.table.tsv: Processed input tables for downstream enrichment.

Contact

Maintained by [Chenqing Zheng]. Contributions, issues, and pull requests are welcome via the GitHub repository.