Systemic analysis of changes in protein modification and gene coexpression networks in cancer

Perturbed posttranslational modification (PTM) landscapes and gene expression networks commonly cause pathological phenotypes. To elucidate altered PTM landscapes on a large scale, disease-associated mutations from TCGA, Uniprot, and dbSNP were integrated with PTM sites from PhosphoSitePlus. We characterized each dataset individually, compared somatic with germline mutations, and analyzed PTM sites intersecting directly with disease variants. To assess the impact of mutations in the flanking regions of phosphosites, we developed DeltaScansite, a pipeline that compares Scansite predictions on wild type versus mutated sequences. Disease mutations are also visualized in PhosphoSitePlus. TCGA also curates gene expression data from tumor and normal tissues, enabling us to calculate gene coexpression networks and apply graph algorithms in Neo4j.

Name thesis:degree_name

Master

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2019

Author dc:creator

• Simpson, Claire M.

Advisor dc:contributor.advisor

• Douglas Lauffenburger and Florian Gnad.

• Electrical Engineering and Computer Science.

Statement dc:rights

• MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

https://hdl.handle.net/1721.1/124262

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/124262