Gene expression analysis of native and invasive populations Centaurea diffusa under control and drought treatments

Mixed effects model analysis of gene expression for native and invasive populations of Centaurea diffusa (diffuse knapweed) in control and drought treatments, from three time points. From unpublished chapter of dissertation, contact me. Transcriptomes and array described in Lai et al., Am J Bot, 2012.

Table S2: LRTsandTAIRaccesssions.xlsx Results from likelihood ratio tests for genes with significant model terms. LRTs are reported for each fixed effect term in mixed effect models of gene expression, for all 11,047 genes with at least one significant fixed effect (α=0.05). Q values corrected for multiple comparisons are reported for each LRT. TAIR 10 accessions (The Arabidopsis Information Resource; arabidopsis.org) and GO term mappings are included where possible.

Table S3: GOresults_sigTrt_pc.slsx GO terms for gene with a significant effect of drought treatment. Results of Fisher’s exact tests examining the number of gene associations with GO terms. Genes of interest were determined in mixed model analysis to have a significant differences between control and drought treatments. Ontology type is indicated for each term; here, biological process only (BP). The analysis was conducted using the Fisher algorithm and parent-child method in topGO, and P-values for this test are reported. Direction of expression was determined by relative range level averages of expression all first time point samples, before onset of treatment, and is expressed in terms of invasive relative to native samples. Separate topGO analyses of up or down regulated genes were then used to confirm association with GO terms.