Identification of potential constitutive and tissue-specific promoters and regulatory motifs in Glycine max through datamining of publicly available sequence data

Keating, Kathleen

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https://hdl.handle.net/2142/42489 Copy

Description

Title

Identification of potential constitutive and tissue-specific promoters and regulatory motifs in Glycine max through datamining of publicly available sequence data

Author(s)

Keating, Kathleen

Issue Date

2013-02-03T19:47:34Z

Director of Research (if dissertation) or Advisor (if thesis)

Hudson, Matthew E.

Department of Study

Crop Sciences

Discipline

Bioinformatics

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(s)

• bioinformatics
• transcription
• datamining
• regulatory motifs
• soybean
• promoters

Abstract

This is a study of gene regulation in soybean (Glycine max), specifically at the level of transcription. Analysis was performed on publicly available soybean EST data, deposited in the NCBI UniGene database, combined with the soybean genome sequence. EST libraries were grouped based on the tissue they were created from. Grouped libraries were selectively filtered to find constitutive, leaf-preferential (not in seed or seed coat), and root-specific transcripts. Transcripts were annotated using G. max and Arabidopsis thaliana databases. Gene ontology term enrichment tools were used to visualize the functions of abundant transcripts for the constitutive, leaf-preferential and root-specific groups. Promoter motif analysis was performed on the promoters for the most highly expressed transcripts of each expression category. The analysis identified many probable constitutive, leaf-preferential and root-specific promoters, as well as several over-represented motifs.

Graduation Semester

2012-12

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http://hdl.handle.net/2142/42489

Copyright and License Information

Copyright 2012 Kathleen Keating

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