Please cite: Jamie A O'Rourke, Luis P Iniguez, Fengli Fu, Bruna Bucciarelli, Susan S Miller, Scott A Jackson, Philip E McClean, Jun Li, Xinbin Dai, Patrick X Zhao, Georgina Hernandez and Carroll P Vance. An RNA-Seq based gene expression atlas of the common bean. BMC Genomics 2014, 15:866.
Welcome to PvGEA
A Common Bean Gene Expression Atlas    
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Search for group of genes

Identify genes with expression levels as RPKM that exceed a cutoff. Select the tissue and the RPKM cutoff value (as an integer).

Look at the gene expression in different tissues

Enter the id of a gene of interest (E.g: Phvul.001G000100.1), a chart of gene expression (in RPKM format) in different tissues will be displayed on the next page.

Download whole dataset

Click the "Raw data" hyperlink to display the total mapped reads per gene per tissue as a tab-delimited text file. Similarly, click the "Normalized data"hyperlink to download the normalized data as RPKM (reads per killobase of sequence per million mapped reads) as a tab-delimited text file.

Look at genes by annotation group

To identify genes by annotations, enter a key word (e.g, nitrogen), all genes with annotations containing the key word will be returned.

Look at the expression chart of a group of genes

Visualize expression of multiple genes, or the different expression level of one gene in different tissues. Letters preceding the gene name can be separated by an underscore. For example, Leaf_Phvul.009G160600.1 represents the expression of gene Phvul.009G160600.1 in leaf while Nodule_Phvul.009G160600.1 represents the expression of the same gene in nodules.

Data & bioinformatic resources were generated by the laboratory of Dr. Carroll P. Vance, USDA-ARS, St. Paul, MN, Dr. Patrick X. Zhao at the Samuel Roberts Noble Foundation, and many international collaborators.