In this thesis I describe the integration of heterogeneous interaction data for Drosophila into DroID, the Drosophilainteractions database, making it a one-stop public resource for interaction data. I have also made it possible to filter the interaction data using gene expression data to generate context-relevant networks making DroID a one-of-a kind resource for biologists. In the two years since the upgraded DroID has been available, several studies have used the heterogeneous interaction data in DroID to advance our understanding of Drosophila biology thus validating the need for such a resource for biologists. In addition to this, I have identified organizing principles of interaction networks based on genome-wide gene expression data in the tissues and the entire life cycle of Drosophila. I have shown that all tissues and stages have a core ubiquitously expressed PPI network to which tissue and stage specific proteins attach to potentially modulate specific functions. In view of these organizing principles, I developed a normalized expression filter for interaction networks. I have shown that networks generated by using this filter are context-relevant as evidenced by their enrichment for genes with relevant mutant phenotypes. This filter has been implemented in DroID and I anticipate that studies on interactome networks using this filter will further our understanding of biology.
","abstract_html":"<p>In this thesis I describe the integration of heterogeneous interaction data for <i>Drosophila</i> into DroID, the <i>Drosophila</i>interactions database, making it a one-stop public resource for interaction data. I have also made it possible to filter the interaction data using gene expression data to generate context-relevant networks making DroID a one-of-a kind resource for biologists. In the two years since the upgraded DroID has been available, several studies have used the heterogeneous interaction data in DroID to advance our understanding of <i>Drosophila</i> biology thus validating the need for such a resource for biologists. In addition to this, I have identified organizing principles of interaction networks based on genome-wide gene expression data in the tissues and the entire life cycle of <i>Drosophila</i>. I have shown that all tissues and stages have a core ubiquitously expressed PPI network to which tissue and stage specific proteins attach to potentially modulate specific functions. In view of these organizing principles, I developed a normalized expression filter for interaction networks. I have shown that networks generated by using this filter are context-relevant as evidenced by their enrichment for genes with relevant mutant phenotypes. This filter has been implemented in DroID and I anticipate that studies on interactome networks using this filter will further our understanding of biology.</p>","abstract_has_math":false,"creators":["Murali, Thilakam"],"institution":null,"degree_name":"Ph.D.","degree_level":"Open Access Dissertation","degree_discipline":"Molecular Biology and Genetics","degree_department":null,"school":null,"contributors":["Russell L. Finley Jr."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2013,"date_issued":"2013-01-02T08:00:00Z","date_published":"2013-01-02T08:00:00Z","updated_at":"2026-07-24T05:59:26Z","subjects":["Data integration","Drosophila","Drosophila Interactions Database","Interaction network","Protein-protein interactions","scaling/ normalization of gene expression","Bioinformatics","Genetics","Molecular Biology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.wayne.edu/oa_dissertations/788","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Russell L. 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I have also made it possible to filter the interaction data using gene expression data to generate context-relevant networks making DroID a one-of-a kind resource for biologists. In the two years since the upgraded DroID has been available, several studies have used the heterogeneous interaction data in DroID to advance our understanding of Drosophila biology thus validating the need for such a resource for biologists. In addition to this, I have identified organizing principles of interaction networks based on genome-wide gene expression data in the tissues and the entire life cycle of Drosophila. I have shown that all tissues and stages have a core ubiquitously expressed PPI network to which tissue and stage specific proteins attach to potentially modulate specific functions. In view of these organizing principles, I developed a normalized expression filter for interaction networks. I have shown that networks generated by using this filter are context-relevant as evidenced by their enrichment for genes with relevant mutant phenotypes. This filter has been implemented in DroID and I anticipate that studies on interactome networks using this filter will further our understanding of biology.
"]},{"key":"dc:title","label":"Title","values":["The Drosophila Interactions Database: Integrating The Interactome And Transcriptome"]}]}],"canonical_facts":{"dc:contributor":["Russell L. Finley Jr."],"dc:creator":["Murali, Thilakam"],"dc:date.available":["2013-01-01T08:00:00Z"],"dc:description.abstract":["In this thesis I describe the integration of heterogeneous interaction data for Drosophila into DroID, the Drosophilainteractions database, making it a one-stop public resource for interaction data. I have also made it possible to filter the interaction data using gene expression data to generate context-relevant networks making DroID a one-of-a kind resource for biologists. In the two years since the upgraded DroID has been available, several studies have used the heterogeneous interaction data in DroID to advance our understanding of Drosophila biology thus validating the need for such a resource for biologists. In addition to this, I have identified organizing principles of interaction networks based on genome-wide gene expression data in the tissues and the entire life cycle of Drosophila. I have shown that all tissues and stages have a core ubiquitously expressed PPI network to which tissue and stage specific proteins attach to potentially modulate specific functions. In view of these organizing principles, I developed a normalized expression filter for interaction networks. I have shown that networks generated by using this filter are context-relevant as evidenced by their enrichment for genes with relevant mutant phenotypes. This filter has been implemented in DroID and I anticipate that studies on interactome networks using this filter will further our understanding of biology.
"],"dc:identifier":["https://digitalcommons.wayne.edu/oa_dissertations/788"],"dc:subject":["Data integration","Drosophila","Drosophila Interactions Database","Interaction network","Protein-protein interactions","scaling/ normalization of gene expression","Bioinformatics","Genetics","Molecular Biology"],"dc:title":["The Drosophila Interactions Database: Integrating The Interactome And Transcriptome"],"thesis:degree_discipline":["Molecular Biology and Genetics"],"thesis:degree_level":["Open Access Dissertation"],"thesis:degree_name":["Ph.D."]},"updated_at":"2026-07-24T05:59:26Z"}