Systems analysis of seed filling in Arabidopsis: using general linear modeling to assess concordance of transcript and protein expression.
Previous systems analyses in plants have focused on a single developmental stage or time point, although it is often important to additionally consider time-index changes. During seed development a cascade of events occurs within a relatively brief time scale. We have collected protein and transcript expression data from five sequential stages of Arabidopsis (Arabidopsis thaliana) seed development encompassing the period of reserve polymer accumulation. Protein expression profiling employed two-dimensional gel electrophoresis coupled with tandem mass spectrometry, while transcript profiling used oligonucleotide microarrays. Analyses in biological triplicate yielded robust expression information for 523 proteins and 22,746 genes across the five developmental stages, and established 319 protein/transcript pairs for subsequent pattern analysis. General linear modeling was used to evaluate the protein/transcript expression patterns. Overall, application of this statistical assessment technique showed concurrence for a slight majority (56%) of expression pairs. Many specific examples of discordant protein/transcript expression patterns were detected, suggesting that this approach will be useful in revealing examples of posttranscriptional regulation.
Hajduch
Martin
M
Department of Biochemistry and Interdisciplinary Plant Group, Plant Genetics Research Unit, Department of Agriculture, Agricultural Research Service, Columbia, MO 65211, USA.
Hearne
Leonard B
LB
Miernyk
Jan A
JA
Casteel
Jill E
JE
Joshi
Trupti
T
Agrawal
Ganesh K
GK
Song
Zhao
Z
Zhou
Mingyi
M
Xu
Dong
D
Thelen
Jay J
JJ
D017360:Arabidopsis / Q000196:embryology*; D015180:Electrophoresis, Gel, Two-Dimensional; D005227:Fatty Acids / Q000378:metabolism; D020869:Gene Expression Profiling; D016014:Linear Models; D010940:Plant Proteins / Q000378:metabolism*; D040901:Proteomics; D012333:RNA, Messenger / Q000378:metabolism*; D012639:Seeds / Q000378:metabolism*; D053719:Tandem Mass Spectrometry
D005227:Fatty Acids; D010940:Plant Proteins; D012333:RNA, Messenger