📋 Description
It would be interesting if TSUMUGI could extract gene networks based not only on phenotypic similarity, but also on opposite phenotypic directions.
Currently, genes are mainly connected when their KO mice show similar phenotypic profiles. However, genes whose KO phenotypes are directionally opposite may also be biologically informative, because they may represent genes that function in opposing pathways, compensatory mechanisms, or feedback relationships.
Example
For example:
-
Gene A KO mice show:
- decreased blood glucose level
- decreased bone mineral density
-
Gene B KO mice show:
- increased blood glucose level
- increased bone mineral density
In this case, the phenotypes of Gene A KO and Gene B KO are opposite in direction. This may suggest that Gene A and Gene B are functionally linked, potentially through reciprocal regulation or feedback mechanisms.
Proposed feature
Add an option to detect and visualize gene pairs or gene networks with opposite phenotypic effects.
Possible implementation ideas:
- Calculate phenotype similarity while considering the direction of phenotypic change.
- Define an “opposite phenotype score” for gene pairs.
- Allow users to switch between:
- similar phenotype networks
- opposite phenotype networks
- Visualize opposite relationships with a different edge style or color.
Expected benefit
This feature may help identify gene pairs or modules that regulate the same biological processes in opposite directions. Such networks could be useful for exploring feedback regulation, compensatory pathways, and functional antagonism between genes.
🔖 TSUMUGI Version
1.0.2
📎 Anything else?
No response
📋 Description
It would be interesting if TSUMUGI could extract gene networks based not only on phenotypic similarity, but also on opposite phenotypic directions.
Currently, genes are mainly connected when their KO mice show similar phenotypic profiles. However, genes whose KO phenotypes are directionally opposite may also be biologically informative, because they may represent genes that function in opposing pathways, compensatory mechanisms, or feedback relationships.
Example
For example:
Gene A KO mice show:
Gene B KO mice show:
In this case, the phenotypes of Gene A KO and Gene B KO are opposite in direction. This may suggest that Gene A and Gene B are functionally linked, potentially through reciprocal regulation or feedback mechanisms.
Proposed feature
Add an option to detect and visualize gene pairs or gene networks with opposite phenotypic effects.
Possible implementation ideas:
Expected benefit
This feature may help identify gene pairs or modules that regulate the same biological processes in opposite directions. Such networks could be useful for exploring feedback regulation, compensatory pathways, and functional antagonism between genes.
🔖 TSUMUGI Version
1.0.2
📎 Anything else?
No response