Maize Genomics Resource
At the University of Georgia
MGR Project Gene Expression Values and Analyses
The Buell Research Group at the University of Georgia has conducted functional annotation of the B73 v4 genome and performed gene expression analyses using the AGPv4 annotation and publicly available RNA-sequencing experiments.
The RNA-sequencing experiment information, gene expression values, differential expression analyses, and weighted gene co-expression analyses are available to download below. The genome annotation and RNA-seq coverage can also be viewed in the JBrowse genome browser. A BLAST server is also available for searching your sequences against B73 v2 through v4 genome and annotation.
For more information on our methods, see Hoopes et al. (2018).
RNA-seq Gene Expression Data
RNA-seq reads were mapped to the v4 genome assembly with TopHat2 (v2.0.14) (Kim et al., 2013) and Bowtie2 (v2.2.3) (Langmead and Salzberg, 2012). Gene expression for the AGPv4 genes was calculated as FPKM using Cufflinks (v2.2.1) (Trapnell et al., 2010).
- Zea_mays.MSU.RNA-seq.libraries.xlsx - Description of the RNA-sequencing experiments and libraries analyzed
- Zea_mays.MSU.FKPM.matrix.txt.gz - Raw FPKM values for AGPv4 genes.
- Zea_mays.MSU.FKPM.matrix.log2.flt1.txt.gz - Log2 transformed FPKM values filtered for genes with an FPKM value > 1 in at least one library.
Differential Gene Expression Analyses
Gene counts were obtained from the RNA read alignments using HTSeq (v0.9.1) (Anders et al., 2015) and compared against each sample's respective control to determine differential gene expression with DESeq2 (Love et al., 2014). A gene was identified as tissue specific if it had a log2 fold change > 2 and an adjusted p-value < 0.01 in the tissue of interest compared to all other tissue types. A gene was identified as differentially expressed under a stress condition if it had a log2 fold change > 2 or < -2 and an adjusted p-value < 0.01 compared to its respective control.
- Zea_mays.tissue.DESeq2.txt.gz - Organ-specific gene expression results.
- Zea_mays.tissue.intraSeed.DESeq2.txt.gz - Endosperm and embryo-specific gene expression results.
- Zea_mays.tissue.intraReproductive.DESeq2.txt.gz - Anther, tassel, and cob-specific gene expression results.
- Zea_mays.stress.DESeq2.txt.gz - Stress induced differential expression results.
Weighted Gene Co-Expression Analysis
Genes containing an FPKM value > 5 in at least one library were log2 transformed and filtered by a coefficient of variance threshold of 0.6. The filtered and transformed FPKM values were used in the WGCNA R package (Langfelder and Horvath, 2008) to generate a weighted gene co-expression network and 12 gene modules.
- Zea_mays.WGCNA.gene.list.tar.gz - AGPv4 genes in each module.
- Zea_mays.WGCNA.FPKM.matrix.tar.gz - Log2 transformed FPKM values for the genes in each module.
- Zea_mays.WGCNA.Z_score.matrix.tar.gz - Z score expression values for the genes in each module.
- Zea_mays.WGCNA.Z_score.graph.tar.gz - Z score expression values graphed by library.
- Zea_mays.WGCNA.connectivity.txt.gz - Gene connectivity values for each module.
NAM Parents RNA-seq Gene Expression Data
RNA-seq data from Diepenbrock et al. 2017 representing a kernel development series, root, and shoot samples from the NAM parents have been mapped to v4 of B73 and expression abundances determined using the same pipeline as described by Hoopes et al. 2018.
- NAM_parents.RNA-seq.FPKM.matrix.xlsx - Matrix of FPKM values for the AGPv4 genes for the NAM parents RNA-seq libraries. (xls file)
Contact:
Dr. C. Robin Buell, University of Georgia - (https://buell-lab.github.io)