Difference between revisions of "Pharmaceutical Compounds analysis"
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==== Description ==== | ==== Description ==== | ||
| − | + | This method seeks for the optimal combination of molecular targets among input genes that potentially interact with pharmaceutical compounds from a library of known drugs and biologically active chemical compounds predicted with the cheminformatics tool PASS. | |
==== Parameters: ==== | ==== Parameters: ==== | ||
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* '''Weight column''' (expert) – Genes<nowiki>'</nowiki> weight column name | * '''Weight column''' (expert) – Genes<nowiki>'</nowiki> weight column name | ||
* '''Diseases names''' – Names of the diseases, all diseases will be considered if nothing is selected | * '''Diseases names''' – Names of the diseases, all diseases will be considered if nothing is selected | ||
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* '''Minimal targets''' – Minimal targets linked with structure satisfying conditions | * '''Minimal targets''' – Minimal targets linked with structure satisfying conditions | ||
* '''Use custom targets threshold''' – Flag to show that targets threshold is enabled. If disabled would be cut off if Pa<Pi | * '''Use custom targets threshold''' – Flag to show that targets threshold is enabled. If disabled would be cut off if Pa<Pi | ||
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* '''Use custom diseases threshold''' – Flag to show that diseases threshold is enabled. If disabled would be cut off if Pa<Pi | * '''Use custom diseases threshold''' – Flag to show that diseases threshold is enabled. If disabled would be cut off if Pa<Pi | ||
* '''Diseases threshold (Pb)''' – Threshold (Pb) to cut off structures with Pa<Pb for all effects which corresponds to selected diseases | * '''Diseases threshold (Pb)''' – Threshold (Pb) to cut off structures with Pa<Pb for all effects which corresponds to selected diseases | ||
| + | * '''False positive target weight''' (expert) – Weight of false positive targets in target activity score formula. False positive targets are known targets of the drug that are not included in input targets list | ||
* '''Output table with structures''' – Output table with structures | * '''Output table with structures''' – Output table with structures | ||
* '''Output table with targets''' – Output table with targets | * '''Output table with targets''' – Output table with targets | ||
Latest revision as of 18:15, 9 December 2020
- Analysis title
Pharmaceutical Compounds analysis
- Provider
- Biosoft
- Class
PCAnalysis- Plugin
- biouml.plugins.genomeenhancer (Genome Enhancer)
[edit] Description
This method seeks for the optimal combination of molecular targets among input genes that potentially interact with pharmaceutical compounds from a library of known drugs and biologically active chemical compounds predicted with the cheminformatics tool PASS.
[edit] Parameters:
- Genes table – Path to table with genes
- Weight column (expert) – Genes' weight column name
- Diseases names – Names of the diseases, all diseases will be considered if nothing is selected
- Minimal targets – Minimal targets linked with structure satisfying conditions
- Use custom targets threshold – Flag to show that targets threshold is enabled. If disabled would be cut off if Pa<Pi
- Targets threshold (Pm) – Threshold (Pm) to cut off targets with Pa<Pm
- Toxicities threshold (Pt) – Threshold (Pt) to cut off structures with Pa>Pt for at least one toxicity
- Use custom diseases threshold – Flag to show that diseases threshold is enabled. If disabled would be cut off if Pa<Pi
- Diseases threshold (Pb) – Threshold (Pb) to cut off structures with Pa<Pb for all effects which corresponds to selected diseases
- False positive target weight (expert) – Weight of false positive targets in target activity score formula. False positive targets are known targets of the drug that are not included in input targets list
- Output table with structures – Output table with structures
- Output table with targets – Output table with targets
