Overlap between DEGs found at the three stages

DEGs expression change across all stages

Genes coherently changing in the two stages in the plot (i.e. l2FC>=0.05 or <=-0.05 in both stages and with at least abs(l2FC)>=0.1 in one of the two stages) are colored and labeled.

FIGURE

Genes coherently changing in the two stages in the plot (i.e. l2FC>=0.05 or <=-0.05 in both stages and with at least abs(l2FC)>=0.1 in one of the two stages) are colored, genes coherently changing in all three stages (i.e. l2FC>=0.05 or <=-0.05 in all three stages and with at least abs(l2FC)>=0.1 in one of the three stages) are also labeled.

Correlations - all DEGs

cor(DEGs_res_all_preimpl_activeVsDead_merged$log2FoldChange.twocell, DEGs_res_all_preimpl_activeVsDead_merged$log2FoldChange.morulae, method = "pearson")
## [1] 0.007678755
cor(DEGs_res_all_preimpl_activeVsDead_merged$log2FoldChange.twocell, DEGs_res_all_preimpl_activeVsDead_merged$log2FoldChange.blasto, method = "pearson")
## [1] 0.007779939

Correlations - only coherently changing DEGs

coherent_DEGs_twocell_mor_dt <- DEGs_res_all_preimpl_activeVsDead_merged[DEGs_res_all_preimpl_activeVsDead_merged$color_twocell_mor != "none"]
coherent_DEGs_twocell_blasto_dt <- DEGs_res_all_preimpl_activeVsDead_merged[DEGs_res_all_preimpl_activeVsDead_merged$color_twocell_blasto != "none"]

cor(coherent_DEGs_twocell_mor_dt$log2FoldChange.twocell, coherent_DEGs_twocell_mor_dt$log2FoldChange.morulae, method = "pearson")
## [1] 0.6118887
cor(coherent_DEGs_twocell_blasto_dt$log2FoldChange.twocell, coherent_DEGs_twocell_blasto_dt$log2FoldChange.blasto, method = "pearson")
## [1] 0.2175304
sessionInfo()
## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] gplots_3.1.3                data.table_1.14.6          
##  [3] ggrepel_0.9.2               ggplot2_3.4.0              
##  [5] DESeq2_1.34.0               SummarizedExperiment_1.24.0
##  [7] Biobase_2.54.0              MatrixGenerics_1.6.0       
##  [9] matrixStats_0.62.0          GenomicRanges_1.46.1       
## [11] GenomeInfoDb_1.30.1         IRanges_2.28.0             
## [13] S4Vectors_0.32.4            BiocGenerics_0.40.0        
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.4.4             sass_0.4.2             bit64_4.0.5           
##  [4] jsonlite_1.8.3         splines_4.1.3          gtools_3.9.3          
##  [7] bslib_0.4.1            assertthat_0.2.1       highr_0.9             
## [10] blob_1.2.3             GenomeInfoDbData_1.2.7 yaml_2.3.6            
## [13] pillar_1.8.1           RSQLite_2.2.18         lattice_0.20-45       
## [16] glue_1.6.2             digest_0.6.30          RColorBrewer_1.1-3    
## [19] XVector_0.34.0         colorspace_2.0-3       htmltools_0.5.3       
## [22] Matrix_1.5-3           XML_3.99-0.12          pkgconfig_2.0.3       
## [25] genefilter_1.76.0      zlibbioc_1.40.0        xtable_1.8-4          
## [28] scales_1.2.1           BiocParallel_1.28.3    tibble_3.1.8          
## [31] annotate_1.72.0        KEGGREST_1.34.0        farver_2.1.1          
## [34] generics_0.1.3         withr_2.5.0            cachem_1.0.6          
## [37] cli_3.4.1              survival_3.2-13        magrittr_2.0.3        
## [40] crayon_1.5.2           memoise_2.0.1          evaluate_0.18         
## [43] fansi_1.0.3            tools_4.1.3            lifecycle_1.0.3       
## [46] stringr_1.4.1          locfit_1.5-9.6         munsell_0.5.0         
## [49] DelayedArray_0.20.0    AnnotationDbi_1.56.2   Biostrings_2.62.0     
## [52] compiler_4.1.3         jquerylib_0.1.4        caTools_1.18.2        
## [55] rlang_1.0.6            grid_4.1.3             RCurl_1.98-1.9        
## [58] rstudioapi_0.14        labeling_0.4.2         bitops_1.0-7          
## [61] rmarkdown_2.18         codetools_0.2-18       gtable_0.3.1          
## [64] DBI_1.1.3              R6_2.5.1               knitr_1.40            
## [67] dplyr_1.0.10           fastmap_1.1.0          bit_4.0.5             
## [70] utf8_1.2.2             KernSmooth_2.23-20     stringi_1.7.8         
## [73] parallel_4.1.3         Rcpp_1.0.9             vctrs_0.5.1           
## [76] geneplotter_1.72.0     png_0.1-7              tidyselect_1.2.0      
## [79] xfun_0.35