Reimplementation of the Connectivity Map with Accessibility Enhancements

Evren ARICANLI

Bachelor's thesis

Abstract:

The Connectivity Map (CMap) is a biomedical research tool which leverages modern biotechnology and bioinformatic methods to provide a platform for comparing the a subject gene expression profile against a library of drug-treatment gene expression profiles. This comparison allows for retrieval of drugs from the CMap's library which induce biological activity similar (or dissimilar) to a given subject expression profile -- thereby making it a tool which allows for the finding of repositionable drugs. Herein, a number of adaptations are proposed -- most focally being changes which would enhance the tool's accessibility (e.g. a simplified UI/workflow, expanded queryable gene identifiers). Using the R statistical computing environment and numerous libraries available through it, an adapted CMap tool was created from the publically-accessible CMap data, which housed the proposed adaptations. To evaluate success of the accessibility adaptations, the adapted CMap tool was focus tested on several participants -- which ultimately yielded great favor for the changes made, allowing them to be conclusively suggested for future iterations of the CMap.

Abstract:

The Connectivity Map (CMap) is a biomedical research tool which leverages modern biotechnology and bioinformatic methods to provide a platform for comparing the a subject gene expression profile against a library of drug-treatment gene expression profiles. This comparison allows for retrieval of drugs from the CMap's library which induce biological activity similar (or dissimilar) to a given subject expression profile -- thereby making it a tool which allows for the finding of repositionable drugs. Herein, a number of adaptations are proposed -- most focally being changes which would enhance the tool's accessibility (e.g. a simplified UI/workflow, expanded queryable gene identifiers). Using the R statistical computing environment and numerous libraries available through it, an adapted CMap tool was created from the publically-accessible CMap data, which housed the proposed adaptations. To evaluate success of the accessibility adaptations, the adapted CMap tool was focus tested on several participants -- which ultimately yielded great favor for the changes made, allowing them to be conclusively suggested for future iterations of the CMap.

Keywords

Connectivity Map, Gene Expression Analysis, DNA microarrays, User Interface Accessibilty, Factor Analysis for Robust Microarray Summarization, Custom Microarray CDFs, Drug Repositioning

Language used: English

Date on which the thesis was submitted / produced: 27. 10. 2020

Thesis defence

• Supervisor: prof. Dr. Sepp Hochreiter

UNIVERSITY OF SOUTH BOHEMIA IN ČESKÉ BUDĚJOVICE

Faculty of Science

Bachelor programme / field:
Applied Informatics / Bioinformatics