University of Illinois Urbana-Champaign

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

Keating, Kathleen

Content Files
Kathleen_Keating.pdf
SupplementalFile1.txt
SupplementalFile2.txt
SupplementalFile3.txt
SupplementalTable1.xlsx
SupplementalTable2.xlsx
SupplementalTable3.xlsx

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

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
Date of Ingest
2013-02-03T19:47:34Z
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
Permalink
http://hdl.handle.net/2142/42489
Copyright and License Information
Copyright 2012 Kathleen Keating

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