TSUMUGI 1.0.0

TSUMUGI: Phenotype-Driven Gene Network Identifier

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TSUMUGI (Trait-driven Surveillance for Mutation-based Gene module Identification) is a web tool that uses knockout (KO) mouse phenotype data from the International Mouse Phenotyping Consortium (IMPC) to extract and visualize gene modules based on phenotypic similarity.

TSUMUGI (紡ぎ) comes from the idea of “weaving together gene groups that form phenotypes.”

This web app is available to everyone online👇️

🔗https://larc-tsukuba.github.io/tsumugi/

📖 How to Use TSUMUGI

TSUMUGI supports three kinds of input.

Phenotype

Enter a phenotype of interest to search for genes whose KO mice have similar overall phenotype profiles.
Phenotype names follow Mammalian Phenotype Ontology (MPO).

👉 Phenotype list

Gene

Specify one gene to search for other genes whose KO mice show similar phenotypes.
Gene symbols follow MGI.

👉 Gene list

Gene List

Paste multiple genes (one per line). This extracts phenotypically similar genes among the genes in the list.

[!CAUTION]
If no similar genes are found: No similar phenotypes were found among the entered genes.
If more than 200 similar genes are found: Too many genes submitted. Please limit the number to 200 or fewer.

📥 Download data

TSUMUGI reports gzipped JSONL files.

genewise_phenotype_annotations.jsonl.gz

• Gene symbol (e.g., "1110059G10Rik")
• Marker accession ID (e.g., "MGI:1913452")
• Phenotype term name/ID (e.g., "fused joints", "MP:0000137")
• Effect size (e.g., 0.0, 1.324)
• Significance flag (true/false)
• Zygosity ("Homo", "Hetero", "Hemi")
• Life stage ("Embryo", "Early", "Interval", "Late")
• Sexual dimorphism ("None", "Male", "Female")
• Disease annotation (e.g., [] or "Premature Ovarian Failure 18")

Example:

{"life_stage": "Early", "marker_symbol": "1110059G10Rik", "marker_accession_id": "MGI:1913452", "effect_size": 0.0, "mp_term_name": "fused joints", "disease_annotation": [], "significant": false, "zygosity": "Homo", "sexual_dimorphism": "None", "mp_term_id": "MP:0000137"}

pairwise_similarity_annotations.jsonl.gz

• Gene pair (gene1_symbol, gene2_symbol)
• phenotype_shared_annotations (per-phenotype metadata: life stage, zygosity, sexual dimorphism)
• phenotype_similarity_score (Phenodigm score, 0–100)

Example:

{"gene1_symbol": "1110059G10Rik", "gene2_symbol": "Cog6", "phenotype_shared_annotations": {"vertebral transformation": {"zygosity": "Homo", "life_stage": "Early", "sexual_dimorphism": "Male"}}, "phenotype_similarity_score": 42}

🌐 Network

The page transitions and draws the network automatically.

[!IMPORTANT]
Gene pairs with 3 or more shared abnormal phenotypes and phenotypic similarity > 0.0 are visualized.

Network panel

Nodes represent genes. Click to see the list of abnormal phenotypes observed in that KO mouse; drag to rearrange positions.
Edges show shared phenotypes; click to view details. Modules outline subnetworks of genes. Click a module to list phenotypes involving its member genes; drag modules to reposition them and avoid overlap.

Control panel

Adjust network display from the left panel.

Filter by phenotypic similarity

Phenotypes similarity slider thresholds edges by Resnik→Phenodigm score.

For how we compute similarity, see: 👉 🔍 How We Calculate Phenotypically Similar Genes

Filter by phenotype severity

Phenotype severity slider filters nodes by effect size (severity in KO mice). Higher values mean stronger impact.

Hidden for binary phenotypes (e.g., abnormal embryo development; binary list here) or single-gene input.

Specify genotype

Choose the genotype in which phenotypes appear:

• Homo: homozygous
• Hetero: heterozygous
• Hemi: hemizygous

Specify sex

Extract sex-specific phenotypes:

• Female
• Male

Specify life stage

Filter by life stage in which phenotypes appear:

• Embryo
• Early (0–16 weeks)
• Interval (17–48 weeks)
• Late (49+ weeks)

Markup panel

Highlight: Human Disease

Highlight genes linked to human disease (IMPC Disease Models Portal data).

Search: Specific Gene

Search gene names within the network.

Layout & Display

Adjust layout, font size, edge width, and node repulsion (Cose layout).

Export

Export the current network as PNG/CSV/GraphML.
CSV includes connected-component (module) IDs and phenotype lists per gene; GraphML is Cytoscape-compatible.

🛠 Command-Line Edition

This release adds a CLI so you can download the latest IMPC updates yourself, rerun TSUMUGI, and apply finer filters and output options.

• Recompute with IMPC statistical-results-ALL.csv.gz (optionally mp.obo, impc_phenodigm.csv).
• Filter by presence/absence of MP terms.
• Filter by gene list (comma-separated or text file).
• Outputs: GraphML (tsumugi build-graphml), offline webapp bundle (tsumugi build-webapp).

Available commands

• tsumugi run: Recompute the network from IMPC data
• tsumugi mp --include/--exclude (--pairwise/--genewise): Filter gene pairs or genes that contain / do not show an MP term
• tsumugi count --pairwise/--genewise (--min/--max): Filter by phenotype counts (pairwise or per gene)
• tsumugi score (--min/--max): Filter by phenotype similarity score (pairwise)
• tsumugi genes --keep/--drop: Keep/drop by gene list (comma-separated or text file)
• tsumugi life-stage --keep/--drop: Filter by life stage (Embryo/Early/Interval/Late)
• tsumugi sex --keep/--drop: Filter by sex (Male/Female/None)
• tsumugi zygosity --keep/--drop: Filter by zygosity (Homo/Hetero/Hemi)
• tsumugi build-graphml: Generate GraphML (Cytoscape, etc.)
• tsumugi build-webapp: Generate TSUMUGI webapp assets (local HTML/CSS/JS)

All filtering subcommands stream JSONL to STDOUT. Redirect with > if you want to save results to a file.

Installation

BioConda:

conda install -c conda-forge -c bioconda tsumugi

PyPI:

pip install tsumugi

You are ready if tsumugi --version prints the version.

Usage

Recompute from IMPC data (tsumugi run)

If --mp_obo is omitted, TSUMUGI uses the bundled data-version: releases/2025-08-27/mp.obo.
If --impc_phenodigm is omitted, it uses the file fetched on 2025-10-01 from the IMPC Disease Models Portal.

tsumugi run \
  --output_dir ./tsumugi-output \
  --statistical_results ./statistical-results-ALL.csv.gz \
  --threads 8

Outputs: ./tsumugi-output contains genewise annotations (genewise_phenotype_annotations.jsonl.gz), pairwise similarity data (pairwise_similarity_annotations.jsonl.gz), and visualization assets (TSUMUGI-webapp).

[!IMPORTANT]
The TSUMUGI-webapp directory includes OS-specific launch scripts; double-click to open the local web app:

• Windows: open_webapp_windows.bat
• macOS: open_webapp_mac.command
• Linux: open_webapp_linux.sh

Filter by MP term (tsumugi mp --include/--exclude)

Extract gene pairs (or genes) that include phenotypes of interest, or pairs whose relevant phenotypes were measured but did not show significant abnormalities.

tsumugi mp [-h] (-i MP_ID | -e MP_ID) [-g | -p] [-m MP_OBO] [-a GENEWISE_ANNOTATIONS] [--in IN] [--life_stage LIFE_STAGE] [--sex SEX] [--zygosity ZYGOSITY]

-i MP_ID, --include MP_ID

Include genes/gene pairs that have the specified MP term (descendants included).

-e MP_ID, --exclude MP_ID

Return genes/gene pairs that were measured for the specified MP term (descendants included) and did not show a significant phenotype. Requires -a/--genewise_annotations.

-g, --genewise

Filter at gene level. Reads genewise_phenotype_annotations.jsonl(.gz). When using --genewise, specify -a/--genewise_annotations.

-p, --pairwise

Filter at gene-pair level. Targets pairwise_similarity_annotations.jsonl(.gz). If --in is omitted, reads from STDIN.

-m MP_OBO, --mp_obo MP_OBO

Path to Mammalian Phenotype ontology (mp.obo). If omitted, uses the bundled data/mp.obo.

-a GENEWISE_ANNOTATIONS, --genewise_annotations GENEWISE_ANNOTATIONS

Path to the genewise annotation file (JSONL/.gz). Required for --exclude; also specify when using --genewise.

--in IN

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

--life_stage LIFE_STAGE

Additional filter by life stage. Available values: Embryo, Early, Interval, Late.

--sex SEX

Additional filter by sexual dimorphism. Use the values present in annotations (e.g., Male, Female, None).

--zygosity ZYGOSITY

Additional filter by zygosity. Available values: Homo, Hetero, Hemi.

# Extract only gene pairs that include MP:0001146 (abnormal testis morphology) or descendant terms (e.g., MP:0004849 abnormal testis size)
tsumugi mp --include MP:0001146 \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_filtered.jsonl

# Extract gene pairs whose measured genes include MP:0001146 and descendant terms and did not show a significant abnormality
tsumugi mp --exclude MP:0001146 \
  --genewise genewise_phenotype_annotations.jsonl.gz \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_filtered.jsonl

# Extract significant gene-level annotations containing MP:0001146 (descendants included)
tsumugi mp --include MP:0001146 \
  --genewise \
  --genewise_annotations genewise_phenotype_annotations.jsonl.gz \
  > genewise_filtered.jsonl

# Extract genes measured for MP:0001146 (descendants included) that did not show a significant abnormality
tsumugi mp --exclude MP:0001146 \
  --genewise \
  --genewise_annotations genewise_phenotype_annotations.jsonl.gz \
  > genewise_no_phenotype.jsonl

[!IMPORTANT] Descendant MP terms of the specified ID are also handled.
For example, if you specify MP:0001146 (abnormal testis morphology), descendant terms such as MP:0004849 (abnormal testis size) are considered as well.

Filter by phenotype counts (tsumugi count)

tsumugi count [-h] (-g | -p) [--min MIN] [--max MAX] [--in IN] [-a GENEWISE_ANNOTATIONS]

Filter genes or gene pairs by the number of phenotypes. At least one of --min or --max is required.

-g, --genewise

Filter by the number of significant phenotypes per gene. Requires -a/--genewise_annotations with genewise_phenotype_annotations.jsonl(.gz).

-p, --pairwise

Filter by the number of shared phenotypes per gene pair. If --in is omitted, reads pairwise_similarity_annotations.jsonl(.gz) from STDIN.

--min MIN, --max MAX

Lower/upper bounds for phenotype counts. Use either flag alone for one-sided filtering.

--in IN

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

-a GENEWISE_ANNOTATIONS, --genewise_annotations GENEWISE_ANNOTATIONS

Path to the genewise annotation file (JSONL/.gz). Required with --genewise.

• Shared phenotypes per pair:

tsumugi count --pairwise --min 3 --max 20 \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_min3_max20.jsonl

• Phenotypes per gene (genewise required):

tsumugi count --genewise --min 5 --max 50 \
  --genewise genewise_phenotype_annotations.jsonl.gz \
  --in pairwise_similarity_annotations.jsonl.gz \
  > genewise_min5_max50.jsonl

--min or --max alone is fine.

Filter by similarity score (tsumugi score)

tsumugi score [-h] [--min MIN] [--max MAX] [--in IN]

Filter gene pairs by phenotype_similarity_score (0–100). At least one of --min or --max is required.

--min MIN, --max MAX

Lower/upper bounds for phenotype similarity score. Use either flag alone for one-sided filtering.

--in IN

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

tsumugi score --min 50 --max 80 \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_score50_80.jsonl

--min or --max alone is fine.

Filter by gene list (tsumugi genes --keep/--drop)

tsumugi genes [-h] (-k GENE_SYMBOL | -d GENE_SYMBOL) [--in IN]

-k GENE_SYMBOL, --keep GENE_SYMBOL

Keep only pairs containing specified genes (comma-separated list or text file).

-d GENE_SYMBOL, --drop GENE_SYMBOL

Drop pairs containing specified genes (comma-separated list or text file).

--in IN

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

tsumugi genes --keep genes.txt \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_keep_genes.jsonl

tsumugi genes --drop geneA,geneB \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_drop_genes.jsonl

Filter by life stage (tsumugi life-stage --keep/--drop)

tsumugi life-stage [-h] (-k LIFE_STAGE | -d LIFE_STAGE) [--in IN]

-k LIFE_STAGE, --keep LIFE_STAGE

Keep only annotations with the specified life stage (Embryo, Early, Interval, Late).

-d LIFE_STAGE, --drop LIFE_STAGE

Drop annotations with the specified life stage.

--in IN

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

tsumugi life-stage --keep Early \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_lifestage_early.jsonl

Filter by sex (tsumugi sex --keep/--drop)

tsumugi sex [-h] (-k SEX | -d SEX) [--in IN]

-k SEX, --keep SEX

Keep only annotations with the specified sexual dimorphism (Male, Female, None).

-d SEX, --drop SEX

Drop annotations with the specified sexual dimorphism.

--in IN

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

tsumugi sex --drop Male \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_no_male.jsonl

Filter by zygosity (tsumugi zygosity --keep/--drop)

tsumugi zygosity [-h] (-k ZYGOSITY | -d ZYGOSITY) [--in IN]

-k ZYGOSITY, --keep ZYGOSITY

Keep only annotations with the specified zygosity (Homo, Hetero, Hemi).

-d ZYGOSITY, --drop ZYGOSITY

Drop annotations with the specified zygosity.

--in IN

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

tsumugi zygosity --keep Homo \
  --in pairwise_similarity_annotations.jsonl.gz \
  > pairwise_homo.jsonl

Export GraphML / webapp

tsumugi build-graphml [-h] [--in IN] -a GENEWISE_ANNOTATIONS

--in IN

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

-a GENEWISE_ANNOTATIONS, --genewise_annotations GENEWISE_ANNOTATIONS

Path to the genewise annotation file (JSONL/.gz). Required.

tsumugi build-graphml \
  --in pairwise_similarity_annotations.jsonl.gz \
  --genewise genewise_phenotype_annotations.jsonl.gz \
  > network.graphml

tsumugi build-webapp [-h] [--in IN] -a GENEWISE_ANNOTATIONS -o OUT

--in IN

Path to the pairwise annotation file (JSONL/.gz). If omitted, reads from STDIN.

-a GENEWISE_ANNOTATIONS, --genewise_annotations GENEWISE_ANNOTATIONS

Path to the genewise annotation file (JSONL/.gz). Required.

-o OUT, --out OUT

Output directory for the webapp bundle (HTML/CSS/JS + network data). Do not specify a filename with an extension.

tsumugi build-webapp \
  --in pairwise_similarity_annotations.jsonl.gz \
  --genewise genewise_phenotype_annotations.jsonl.gz \
  --output_dir ./webapp_output

CLI supports STDIN/STDOUT, so you can chain commands:
zcat pairwise_similarity_annotations.jsonl.gz | tsumugi mp ... | tsumugi genes ... > out.jsonl

🔍 How We Calculate Phenotypically Similar Genes

Data source

IMPC Release-23.0 statistical-results-ALL.csv.gz
Columns: Data fields

Preprocessing

Extract gene–phenotype pairs with KO mouse P-value (p_value, female_ko_effect_p_value, or male_ko_effect_p_value) ≤ 0.0001.

• Annotate genotype-specific phenotypes: homo, hetero, hemi
• Annotate sex-specific phenotypes: female, male

Phenotypic similarity

TSUMUGI currently follows a Phenodigm-like approach (Smedley D, et al. (2013)). We compute Resnik similarity between MP terms and Jaccard similarity between term sets, then combine them by the geometric mean. The key difference from the original Phenodigm is that TSUMUGI adds metadata weighting (zygosity, life stage, sexual dimorphism) when aggregating similarities.

1. Build the MP ontology and compute Information Content(IC) for each term:
   IC(term) = -log((|Descendants(term)| + 1) / |All MP terms|)
   Terms below the 5th percentile of IC are set to 0.
2. For each MP term pair, find the most specific common ancestor and compute Resnik similarity as its IC.
   Compute Jaccard index over the ancestor sets.
   Pairwise term similarity = sqrt(Resnik * Jaccard).
3. For each gene pair, build a term-by-term similarity matrix and apply metadata weighting.
   Zygosity, life stage, and sexual dimorphism matches contribute weights of 0.25/0.5/0.75/1.0 for 0/1/2/3 matches.
4. Apply Phenodigm-style scaling to 0–100:
   Use row/column maxima to get actual max and mean similarity.
   Normalize by theoretical max/mean based on IC, then compute
   Score = 100 * (normalized_max + normalized_mean) / 2.
   If a theoretical denominator is 0, that term is set to 0.

✉️ Contact

• Google Form: https://forms.gle/ME8EJZZHaRNgKZ979
• GitHub Issues: https://github.com/akikuno/TSUMUGI-dev/issues/new/choose