Pathway improvements in cBioPortal

[ugurdogrusoz]

Background:

Pathway diagrams are widely used in genomics to describe changes occurring in signaling pathways resulting from genomic alterations. There are several tools available to facilitate the visualization and analysis of pathway alterations, including PathwayMapper.

PathwayMapper is a collaborative visual web editor for cancer pathways and genomics data, that also allows users to enrich pathway diagrams by overlaying genomic alteration data, and provides an interactive graphical editing tool for creating and modifying pathways.

PathwayMapper [1] has also been integrated into the cBioPortal for Cancer Genomics, an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. For an overview on the cBioPortal, please refer to the home page.

When users query a cancer study on the cBioPortal for genes of interest, they are taken to a new page containing various visualizations and reports for analysis that users can navigate to by selecting the desired tab. The Pathways tab is where users can view the available cancer pathways which are matched to the genes of interest by count or percentage and ranked using this score. See the example provided below and/or follow this link to see the Results page and available reports/visualizations yourself.

Figure 1. Example Pathways tab view. Queried genes: TP53, KRAS, PIK3CA, TERT.

Last summer, the Pathways tab was also added to the Comparison Page in cBioPortal, where map frequencies in different groups are overlaid on to the pathway objects, further integrating its use in the portal.

Figure 2. Example Pathways tab view in the Comparison Page with two groups.

While highly useful, the integration of PathwayMapper into the cBioPortal can be further improved through the addition of features like allowing users to overlay data on pathways on the fly, for example.

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Goal:

The goal of this project is to improve the integration of PathwayMapper into cBioPortal as well as enhancing the full-blown, stand-alone editor version as follows.

PathwayMapper viewer in cBioPortal

• Currently available pathways are matched to genes of interest by count or percentage and ranked using this score. Alternative or better ranking schemes should be investigated and implemented.

• Resolve several miscellaneous outstanding issues/bugs

PathwayMapper editor

• The overall architecture should be revisited to properly address different views in different context (e.g. full PathwayMapper editor vs PathwayMapper in Comparison Page, Patient View and Results page).

• Expand-collapse and hide-show operations should be integrated (via associated Cytoscape.js extensions) for complexity management.

• Filtering (by alteration percentage) and highlighting capabilities should be incorporated.

• Collaborative mode in the editor is based on SharedDB and seems to work OK for the most part but every now and then it breaks. This is a serious issue that needs to be carefully debugged and fixed.

• All third party libraries need to be upgraded.

• Resolve several miscellaneous outstanding issues/bugs

[1] I. Bahceci, U. Dogrusoz, K.C. La, Ö. Babur, J. Gao, N. Schultz, "PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data", Bioinformatics, 33(14), pp. 2238-2240, 2017.

Approach:

This project requires you to work on both PathwayMapper and cBioPortal repositories and be mostly experience in doing front-end work.

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Needed skills:

• Good programming skills and experience in web technologies (JavaScript, html, css)
• Knowledge of React is required
• Familiarity with visualization software is a big plus. (PathwayMapper is based on Cytoscape.js)

Possible mentors:

@onursumer @ugurdogrusoz

[Abinash-bit]

@ugurdogrusoz Hlo sir ... I am intrested in resolving this issue. Please guide me

[Djokovic0311]

Hi! @ugurdogrusoz I am Jiahang Li, a master student in Computer Science at Boston University. I am really interested in this issue and willing to help with your meaningful community. Could you please guide me?
This is my personal website developed with React.js Jiahang Li Portfolio showing my detailed personal and technical backgrounds. May I ask if there is any sub-issue I can first fix? Or shall I start working on the proposal?

[ugurdogrusoz]

Best way to get started before writing a proposal would be to investigate the code base and architecture of the two related repos (cBio and PathwayMapper).

[Djokovic0311]

Thank you! I have already run the cBioPortal frontend project successfully and understand the basic structures. Now I am diving into the Pathway-mapper and try to make progress. I found in figure 2, there is no pathway tab in the comparision page. Can you please give me some guidance?

[inodb]

@Djokovic0311 ah good catch! The feature is currently still hidden behind a specific URL parameter. Try:

https://www.cbioportal.org/comparison/pathways?sessionId=5cf89323e4b0ab413787436c&groupOrder=%5B%22Primary%22%2C%22Metastasis%22%5D&featureFlags=group_comparison_pathways

It will only show up if you add featureFlags=group_comparison_pathways in the URL. This is something we use for functionality we are still testing out

[Djokovic0311]

@Djokovic0311 ah good catch! The feature is currently still hidden behind a specific URL parameter. Try:

https://www.cbioportal.org/comparison/pathways?sessionId=5cf89323e4b0ab413787436c&groupOrder=%5B%22Primary%22%2C%22Metastasis%22%5D&featureFlags=group_comparison_pathways

It will only show up if you add featureFlags=group_comparison_pathways in the URL. This is something we use for functionality we are still testing out

Thank you for the reply! Got it.

[Shashank2104125]

@inodb , @ugurdogrusoz I am interested in this project. Is this project open for GSoC 2024?