PMID- 18570655
OWN - NLM
STAT- MEDLINE
DCOM- 20080903
LR  - 20230419
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 9
DP  - 2008 Jun 20
TI  - Double feature selection and cluster analyses in mining of microarray data from 
      cotton.
PG  - 295
LID - 10.1186/1471-2164-9-295 [doi]
AB  - BACKGROUND: Cotton fiber is a single-celled seed trichome of major biological and 
      economic importance. In recent years, genomic approaches such as microarray-based 
      expression profiling were used to study fiber growth and development to 
      understand the developmental mechanisms of fiber at the molecular level. The vast 
      volume of microarray expression data generated requires a sophisticated means of 
      data mining in order to extract novel information that addresses fundamental 
      questions of biological interest. One of the ways to approach microarray data 
      mining is to increase the number of dimensions/levels to the analysis, such as 
      comparing independent studies from different genotypes. However, adding 
      dimensions also creates a challenge in finding novel ways for analyzing 
      multi-dimensional microarray data. RESULTS: Mining of independent microarray 
      studies from Pima and Upland (TM1) cotton using double feature selection and 
      cluster analyses identified species-specific and stage-specific gene transcripts 
      that argue in favor of discrete genetic mechanisms that govern developmental 
      programming of cotton fiber morphogenesis in these two cultivated species. Double 
      feature selection analysis identified the highest number of differentially 
      expressed genes that distinguish the fiber transcriptomes of developing Pima and 
      TM1 fibers. These results were based on the finding that differences in fibers 
      harvested between 17 and 24 day post-anthesis (dpa) represent the greatest 
      expressional distance between the two species. This powerful selection method 
      identified a subset of genes expressed during primary (PCW) and secondary (SCW) 
      cell wall biogenesis in Pima fibers that exhibits an expression pattern that is 
      generally reversed in TM1 at the same developmental stage. Cluster and functional 
      analyses revealed that this subset of genes are primarily regulated during the 
      transition stage that overlaps the termination of PCW and onset of SCW 
      biogenesis, suggesting that these particular genes play a major role in the 
      genetic mechanism that underlies the phenotypic differences in fiber traits 
      between Pima and TM1. CONCLUSION: The novel application of double feature 
      selection analysis led to the discovery of species- and stage-specific genetic 
      expression patterns, which are biologically relevant to the genetic programs that 
      underlie the differences in the fiber phenotypes in Pima and TM1. These results 
      promise to have profound impacts on the ongoing efforts to improve cotton fiber 
      traits.
FAU - Alabady, Magdy S
AU  - Alabady MS
AD  - Functional Genomics Lab, Department of Plant and Soil Science, Texas Tech 
      University, Lubbock, Texas 79409, USA. magdy.alabady@ttu.edu
FAU - Youn, Eunseog
AU  - Youn E
FAU - Wilkins, Thea A
AU  - Wilkins TA
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20080620
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
SB  - IM
MH  - Cluster Analysis
MH  - Cotton Fiber
MH  - Data Interpretation, Statistical
MH  - Gene Expression Profiling
MH  - Gene Expression Regulation, Developmental
MH  - Gene Expression Regulation, Plant
MH  - Genes, Plant
MH  - Gossypium/classification/*genetics/growth & development
MH  - Oligonucleotide Array Sequence Analysis/*statistics & numerical data
MH  - Species Specificity
PMC - PMC2441630
EDAT- 2008/06/24 09:00
MHDA- 2008/09/04 09:00
PMCR- 2008/06/20
CRDT- 2008/06/24 09:00
PHST- 2007/10/11 00:00 [received]
PHST- 2008/06/20 00:00 [accepted]
PHST- 2008/06/24 09:00 [pubmed]
PHST- 2008/09/04 09:00 [medline]
PHST- 2008/06/24 09:00 [entrez]
PHST- 2008/06/20 00:00 [pmc-release]
AID - 1471-2164-9-295 [pii]
AID - 10.1186/1471-2164-9-295 [doi]
PST - epublish
SO  - BMC Genomics. 2008 Jun 20;9:295. doi: 10.1186/1471-2164-9-295.