Data Source


The gene coexpression analysis in RiceFREND is performed based on 24 datasets representing 815 microarray data including redundant data among the datasets. Details on each dataset can be accessed from the RiceXPro database. The data have also been deposited in NCBI’s Gene Expression Omnibus (GEO), and accessible through GEO series accession numbers, GSE21396, GSE21397, GSE36040, GSE36042, GSE36043, GSE36044, GSE39423, GSE39424, GSE39425, GSE39426, GSE39427, GSE39429, and GSE39432. All data were generated using the rice 4x44K microarray RAP-DB platform, which contains 35,760 independent probes corresponding to 27,201 annotated loci published in RAP-DB.

The microarray data were obtained by either one-color (intensity-based) or two-color (ratio-based) hybridization system. For data sets using the one-color method, the processed raw signal intensity of each probe was subjected to 75th percentile normalization and transformed to log2 scale. In addition, the median expression value across the data within each dataset were subtracted for each probe. In the case of multiple probes corresponding to the same locus, the average expression value was used. For microarray data obtained by two-color microarray system, the expression value for each gene was calculated as the log-ratio of signal intensity (log2 Cy5/Cy3).

The microarray data from all datasets were combined into one gene expression matrix data. The weighted Pearson’s correlation coefficient (PCC) was calculated to reduce sample bias that may result from using more data from one organ/tissue sample such as leaf. The mutual rank (MR) was used as an index for coexpression as described in ATTED-II.
Dataset Microarray Analysis No. of data Title
RXP_0001 One-color 143 Spatio-temporal gene expression of various tissues/organs throughout entire growth in the field
RXP_0002 One-color 200 Diurnal and circadian gene expression profile of leaf throughout entire growth
RXP_0003 One-color 51 Leaf gene expression profile throughout entire growth in the field (12:00)
RXP_0004 One-color 34 Leaf gene expression profile throughout entire growth in the field (00:00)
RXP_0005 One-color 28 Leaf gene expression profile during sunrise
RXP_0006 One-color 19 Leaf gene expression profile during sunset
RXP_0007 One-color 14 Root gene expression profile throughout entire growth in the field (12:00)
RXP_0008 One-color 14 Root gene expression profile throughout entire growth in the field (00:00)
RXP_0009 One-color 50 Diurnal and circadian gene expression profile of root
RXP_0010 One-color 54 Gene expression profile during reproductive organ development
RXP_0011 One-color 34 Grain gene expression profile at early developmental stage
RXP_0012 One-color 36 Embryo and Endosperm gene expression profile at ripening stage
RXP_1001 Two-color 15 Root gene expression profile in response to abscisic acid
RXP_1006 Two-color 8 Shoot gene expression profile in response to abscisic acid
RXP_1002 Two-color 15 Root gene expression profile in response to gibberellin
RXP_1007 Two-color 8 Shoot gene expression profile in response to gibberellin
RXP_1003 Two-color 15 Root gene expression profile in response to auxin
RXP_1008 Two-color 8 Shoot gene expression profile in response to auxin
RXP_1004 Two-color 15 Root gene expression profile in response to brassinosteroid
RXP_1009 Two-color 8 Shoot gene expression profile in response to brassinosteroid
RXP_1005 Two-color 15 Root gene expression profile in response to cytokinin
RXP_1010 Two-color 8 Shoot gene expression profile in response to cytokinin
RXP_1011 Two-color 15 Root gene expression profile in response to jasmonic acid
RXP_1012 Two-color 8 Shoot gene expression profile in response to jasmonic acid