Results for session: PRJNA869442

Query Summary

Details
Session Slug ebb65bdc-2302-4140-8662-8ef2442cde03
Dataset PRJNA869442 - 2,4-BPS - homo_sapiens - RNA-seq
Concentration 0, 5.00e-04, 1.00e-03, 1.00e-02, 1.00e-01, 5.00e-01, 1.00e+00, 5.00e+00, 1.00e+01, 5.00e+01, 1.00e+02
Dose units µM
Geneset information File: ConsensusPathDB - pathways - pathways - symbols - genomics - homo_sapiens
Custom file: No
Min size: 20
Max size: 200
Filter gene sets: Yes
Preprocessing Steps Viability analysis: No
Viability column:
Filter features: No
Log dose transform: Yes
Download All .rda Download All .xlsx Download All .tsv
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Geneset Dose-Response Model Results

The results table includes metrics such as p-values, adjusted p-values, AIC, AICc, BIC, and degrees of freedom for geneset dose-response fitted models. DoseRider uses generalized mixed models for dose-response analysis, following US EPA guidelines. Full details are in the FAQ section.

Click on the pathway name to view detailed results for that pathway.

Gene Set Gene Set Size Genes in gene set Best Model Best Model P-value Best Model Adjusted P-value Best Model AICc Best Model BIC BMD Lower Bound BMD Median BMD Upper Bound BMD Mean TCD1 Mean TCD1 Lower TCD1 Upper Null AIC Null AICc Null BIC Null df Linear AIC Linear AICc Linear BIC Linear df Linear ICC Non-linear Fixed AIC Non-linear Fixed AICc Non-linear Fixed BIC Non-linear Fixed df Non-linear Fixed ICC Non-linear Mixed AIC Non-linear Mixed AICc Non-linear Mixed BIC Non-linear Mixed df Non-linear Mixed ICC P-value (Linear) P-value (Non-linear Fixed) P-value (Non-linear Mixed) Adjusted P-value (Linear) Adjusted P-value (Non-linear Fixed) Adjusted P-value (Non-linear Mixed) Optimal Clusters
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Dataset level visualizations

Representation of the top significant pathway genesets from the analysis with DoseRider. The pathways are sorted by the -log(p-value) from those that passed the previous filter. The available plots include: dotplot of top pathways, dose-response heatmap, gene set random effects, top pathway responses, BMD density and peaks, and TCD density and peaks.

Click on the tabs to view the different plots.

Note: The plots are interactive and can be downloaded as PNG images.

Note: DoseRider uses spline-based modeling, which can produce artifacts like J-shaped dose-response curves if knots are misused. Knot placement is user-controlled. For cautionary guidance, see Long (2019).