Inferring the properties of transcription factor regulation

The regulatory targets of transcription factors are costly to directly detect using existing technologies. Many computational models have thus been developed to infer the genes targeted by TFs using gene expression profiles, position weight matrices modeling TF protein binding, histone modifications, and other secondary datasets. We develop a framework for scoring the potential targets of various TFs using models that take the profile of motif hits on the proximity of transcription start sites as input, and describe methods to validate this framework using expression datasets. These models are then extended to include cis-regulatory regions inferred from epigenetic data.

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

2016

Author dc:creator

• Grzadkowski, Michal R

Advisor dc:contributor.advisor

• Manolis Kellis.

• Electrical Engineering and Computer Science.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

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

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/103749

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/103749