ModuleFinder : a computational model for the identification of Cis regulatory modules
Name
62171687-MIT.pdf
Description
Full printable version
Size
2.31 MB
Format
Adobe PDF
Checksum (MD5)
4f86abb30767ead7787ffdeb2f098922
Author(s)
He, Fangxue
Advisor(s)
Marth L. Bulyk.
Alternative Title
Module Finder : a computational model for the identification of Cis regulatory modules
Date Issued
2005
Publisher
Massachusetts Institute of Technology
Abstract
Regulation of gene expression occurs largely through the binding of sequence- specific transcription factors (TFs) to genomic DNA binding sites (BSs). This thesis presents a rigorous scoring scheme, implemented as a C program termed "ModuleFinder", that evaluates the likelihood that a given genomic region is a cis regulatory module (CRM) for an input set of TFs according to its degree of: (1) homotypic site clustering; (2) heterotypic site clustering; and (3) evolutionary conservation across multiple genomes. Importantly, ModuleFinder obtains all parameters needed to appropriately weight the relative contributions of these sequence features directly from the input sequences and TFBS motifs, and does not need to first be trained. Using two previously described collections of experimentally verified CRMs in mammals as validation datasets, we show that ModuleFinder is able to identify CRMs with great sensitivity and specificity. We also evaluated ModuleFinder on a set of DNA binding site data for the human TFs Hepatocyte Nuclear Factor HNF1 [alpha], HNF4 [alpha] and HNF6 and compared its performance with logistic regression and neural network models.
Description
Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2005.
Includes bibliographical references (leaves 55-57).
Subjects
Harvard University--MIT Division of Health Sciences and Technology.
MIT Department
Harvard University--MIT Division of Health Sciences and Technology
Terms of Use
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.
Persistent DSpace Link
