Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles

Plant Molecular Biology
Anil Kumar Nalini ChandranKi-Hong Jung

Abstract

This work suggests 2020 potential candidates in rice for the functional annotation of unannotated genes using meta-analysis of anatomical samples derived from microarray and RNA-seq technologies and this information will be useful to identify novel morphological agronomic traits. Although the genome of rice (Oryza sativa) has been sequenced, 14,365 genes are considered unannotated because they lack putative annotation information. According to the Rice Genome Annotation Project Database ( http://rice.plantbiology.msu.edu/ ), the proportion of functionally characterized unannotated genes (0.35%) is quite limited when compared with the approximately 3.9% of annotated genes with assigned putative functions. Researchers require additional information to help them investigate the molecular mechanisms associated with those unannotated genes. To determine which of them might regulate morphological or physiological traits in the rice genome, we conducted a meta-analysis of expression data that covered a wide range of tissue/organ samples. Overall, 2020 genes showed cultivar-, tissue-, or organ-preferential patterns of expression. Representative candidates from featured groups were validated by RT-PCR, and the GUS reporter system was us...Continue Reading

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Methods Mentioned

BETA
RNA-Seq
chip
genotyping
chips
two-hybrid
tandem
immunoprecipitation
transgenic

Software Mentioned

MapMan
TIGR Multi Experiment Viewer ( MeV
STEME
OGRO
RIV
Affymetrix
Cytoscape
R
affy package
Phyllotaxy

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