Develpment of soybean knowledge base for systems biology studies

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI-COLUMBIA AT AUTHOR'S REQUEST.] Soybean (Glycine max), as an important crop worldwide primarily for protein and oil, has raised great interest in both basic and applied researches. Soybean Knowledge Base (SoyKB) is a comprehensive and integrated platform for soybean translational genomics and molecular breeding research. In SoyKB, we have managed different types of soybean omics data for our collaborators and developed many useful analytical tools. In this thesis, several new features of RNA-Seq data were newly developed for SoyKB isualization analysis. The gene expression data are displayed under transcriptomics chart, scatter plot, heatmap and hierarchical clustering. The gene differential expression data are visualized under the differential expression browser, which includes volcano plot, gene annotation, Venn diagram and the weighted gene correlation network analysis (WGCNA). These visualization and analytical tools provide soybean scientists an integrated and systematic manner to view their data and hypotheses on a higher level. Also, an automated soybean genome upgrade system was developed to synchronize with the latest Phytozome release. For breeding purposes, three tools were developed and applied into field studies, including UCSC genome browser, in silico breeding program and Glycine soja genome browser in order to provide our breeder scientists a wide range of data to compare with their fields.

Name thesis:degree_name

M.S.

Level thesis:degree_level

Masters

Discipline thesis:degree_discipline

Computer science (MU)

Grantor dc:publisher

University of Missouri--Columbia

Year dc:date.issued

2014

Author dc:creator

• Chen, Shiyuan

Advisor dc:contributor.advisor

• Xu, Dong, 1965-

Statement dc:rights

• Access to files is limited to the University of Missouri--Columbia with SSO login.

Language dc:language.iso

eng, English

Handle dc:identifier.uri

https://hdl.handle.net/10355/45736

OAI identifier oai:identifier

oai:mospace.umsystem.edu:10355/45736