Over-representation analysis looks at whether a subset of genes that are differentially expressed (input gene list) associate significantly with certain pathways using a statistical test. In our pathway analysis software, PathVisio , the user can define a criteria to select that input gene list to extract them from the complete dataset (e.g. based on a certain threshold or significance level). But often, researchers have a list of genes that they are interested in without an experiment dataset. In this project, PathVisio will be extended with this basic overrepresentation analysis method and additionally, an online version will be developed for our pathway database WikiPathways.
Goal
PathVisio will be extended with a basic over-representation method that uses a gene list as input and provides a ranked list of pathways as output. The genes in the pathways are highlighted when they are in the input gene list.
Additionally this basic analysis module will also be integrated on WikiPathways. The student will develop a page where the user can provide a list of genes, then the PathVisio statistics module gets called to calculate the over-representation and the result will be shown on WikiPathways. The pathways will be shown in the pathvisiojs viewer and the genes in the input list will be highlighted.
Difficulty Level 2
Extension of PathVisio in Java and development of a front page in WikiPathways (PHP).
Skills
List skills/technologies that the student should be familiar with. Also tag the issue with these.
Java, PHP (essential)
mediawiki, JS (nice to have)
Background
Over-representation analysis looks at whether a subset of genes that are differentially expressed (input gene list) associate significantly with certain pathways using a statistical test. In our pathway analysis software, PathVisio , the user can define a criteria to select that input gene list to extract them from the complete dataset (e.g. based on a certain threshold or significance level). But often, researchers have a list of genes that they are interested in without an experiment dataset. In this project, PathVisio will be extended with this basic overrepresentation analysis method and additionally, an online version will be developed for our pathway database WikiPathways.
Goal
PathVisio will be extended with a basic over-representation method that uses a gene list as input and provides a ranked list of pathways as output. The genes in the pathways are highlighted when they are in the input gene list. Additionally this basic analysis module will also be integrated on WikiPathways. The student will develop a page where the user can provide a list of genes, then the PathVisio statistics module gets called to calculate the over-representation and the result will be shown on WikiPathways. The pathways will be shown in the pathvisiojs viewer and the genes in the input list will be highlighted.
Difficulty Level 2
Extension of PathVisio in Java and development of a front page in WikiPathways (PHP).
Skills
List skills/technologies that the student should be familiar with. Also tag the issue with these.
Java, PHP (essential) mediawiki, JS (nice to have)
Public Repository
https://github.com/wikipathways/wikipathways.org https://github.com/pathvisio/pathvisio
Potential Mentors
Martina Kutmon
Contact
Martina Kutmon