Arabidopsis Th. Root Hair and Mus Musculus Neural Specific Gene Orthologs

Load packages

library(scran)
library(scater)
library(scuttle)
library(ggplot2)
library(cowplot)
library(SingleCellExperiment)

load("~/workspace/c_moor_data/gastrulation/gastrulation_sce.rda") 
#dim: 29452 139331 

#log normalize
sce <- logNormCounts(sce)

RHD2 Orthologs:

##RHD2 Orthologs:
#Duox1
gene <- "ENSMUSG00000033268"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Duox2
gene <- "ENSMUSG00000068452"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Grouped plots for Duox1 and Duox2
gene_group <- c("ENSMUSG00000033268", "ENSMUSG00000068452")
plotExpression(object = sce, features = gene_group, x = "celltype", colour_by ="celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 46038 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene_group, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

RHD6 Orthologs

##RHD6 Orthologs
#Sohlh1
gene <- "ENSMUSG00000059625"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Sohlh2
gene <- "ENSMUSG00000027794"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Group Plots for Sohlh1 and Sohlh2
gene_group <- c("ENSMUSG00000059625", "ENSMUSG00000027794")
plotExpression(object = sce, features = gene_group, x = "celltype", colour_by ="celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 46038 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene_group, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

ACT2 and ACT7 Orthologs:

##ACT2/ACT7 Orthologs: 
#Actg2 (7/9)
#positive regulation of gene expression, mesenchyme migration   
gene <- "ENSMUSG00000059430"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Acta1 (7/9)
#response to mechanical stimulus, skeletal muscle fiber development, mesenchyme migration, Striated Muscle Contraction, Muscle contraction
gene <- "ENSMUSG00000031972"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Acta2 (7/9)
#regulation of wound healing, mesenchyme migration, Smooth Muscle Contraction
gene <- "ENSMUSG00000035783"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Actc1 (7/9)
#actin filament organization, cardiac muscle tissue morphogenesis, mesenchyme migration, multiple signaling, Striated Muscle Contraction
gene <- "ENSMUSG00000068614"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Group Plots for Actg2, Acta1, Acta2, Actc1
gene_group <- c("ENSMUSG00000059430", "ENSMUSG00000031972", "ENSMUSG00000035783", "ENSMUSG00000068614")
plotExpression(object = sce, features = gene_group, x = "celltype", colour_by ="celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 92076 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene_group, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

ATN1 Orthologs:

##ATN1 Orthologs:
#Lyn (1/9)
#positive regulation of neuron projection development, multiple signlaing, oligodendrocyte development, neuron projection development, positive regulation of glial cell proliferation, Nervous system development, immune system
gene <- "ENSMUSG00000042228"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Ptk6 (1/9)
#positive regulation of neuron projection development, signaling, immune system, 
gene <- "ENSMUSG00000038751"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Group Plots for Lyn and Ptk6
gene_group <- c("ENSMUSG00000042228", "ENSMUSG00000038751")
plotExpression(object = sce, features = gene_group, x = "celltype", colour_by ="celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 46038 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene_group, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

ARAC5 and ARAC4 Orthologs

##ARAC5/ARAC4 --  root hair initiation, root hairs play role in detecting mechanical stimulus from rain and guiding signaling toward plant to activate genes for immune response
#Rac2 (7/9)
#Ras signaling pathway, Rap1 signaling pathway, Pathways in cancer, literally every signaling pathway including many involved in immune response 
gene <- "ENSMUSG00000033220"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90))

plotExpression(object = sce, features = gene, x = "celltype", colour_by = "celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 23019 rows containing missing values (geom_point).

ACT8 and ACT2 Orthologs

##ACT8/ACT2: root hair cell tip growth % intercellular transport
#Actrt3 ----  e! (48%, many to many, certainty:NO) 
gene <- "ENSMUSG00000037737"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

plotExpression(object = sce, features = gene, x = "celltype", colour_by = "celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 23019 rows containing missing values (geom_point).

COW1 Orthologs

##COW1: cell tip growth, root epidermal cell differentiation, protein transport, root hair elongation   
#Sec14l2 ---- Flybase (4/9 YY) --- e!(24%, many to many, certainty:NO)
# positive regulation of cholesterol biosynthetic process, regulation of catalytic activity 
gene <- "ENSMUSG00000003585"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Sec14l3 ---- Flybase (4/9 YY) --- e!(24%, many to many, certainty:NO)
gene <- "ENSMUSG00000054986"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Group plots for Sec14l2 and Sec14l3
gene_group <- c("ENSMUSG00000003585", "ENSMUSG00000054986")
plotExpression(object = sce, features = gene_group, x = "celltype", colour_by ="celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 46038 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene_group, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

VLN4 Orthologs

##VLN4 --  actin filament organization  root hair elongation    everything actin
#Gsn -- FlyBase (8/9 YY) e!(30%, m:m, certaintiy:no)
#central nervous system development actin polymerization or depolymerization    striated muscle atrophy cell projection organization     
gene <- "ENSMUSG00000026879"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Scin -- FlyBase (8/9 YY) e!(30%, m:m, certaintiy:no)
#central nervous system development actin polymerization or depolymerization    striated cell projection assembly       cell projection organization     regulation of chondrocyte differentiation  Viral carcinogenesis    
gene <- "ENSMUSG00000002565"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Vil1 -- FlyBase (8/9 YY) e!(30%, m:m, certaintiy:no)
#epidermal growth factor receptor signaling pathway     actin polymerization or depolymerization     
gene <- "ENSMUSG00000026175"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Group plots for Gsn, Scin, and Vil1
gene_group <- c("ENSMUSG00000026879", "ENSMUSG00000002565", "ENSMUSG00000026175")
plotExpression(object = sce, features = gene_group, x = "celltype", colour_by ="celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 69057 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene_group, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

NRAMP2 Orthologs

##NRAMP2: ion transport root morphogenesis  root hair elongation    positive regulation of unidimensional cell growth   
#Slc11a1 ----  Flybase (8/9 YY) e! (43%, many to many, certainty:NO) 
# MAPK cascade  regulation of cytokine production  immune response  ion transport    inflammatory response    defense response to bacterium and protozoan 
gene <- "ENSMUSG00000026177"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

plotExpression(object = sce, features = gene, x = "celltype", colour_by = "celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 23019 rows containing missing values (geom_point).

PIP2-4 Orthologs

##PIP2-4: water transport    response to abscisic acid   root hair elongation     transmembrane 
#Aqp5 ----  Flybase (6/9 NN) e! (30%, many to many, certainty:NO) 
# water transport    pancreatic juice secretion  odontogenesis  transmembrane transport  cellular hypotonic response     Salivary secretion 
gene <- "ENSMUSG00000044217"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Aqp4 ----  Flybase (6/9 NN) e! (30%, many to many, certainty:NO) 
# water transport    sensory perception of sound         regulation of vascular endothelial growth factor production      transmembrane transport    water homeostasis  Bile secretion  Vasopressin-regulated water reabsorption         
gene <- "ENSMUSG00000024411"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Aqp1 ----  Flybase (7/9 YN) e! (30%, many to many, certainty:NO) 
# water transport    glomerular filtration       cellular water homeostasis   transmembrane transport    cellular response to mechanical stimulus    Bile secretion  Renin secretion     Proximal tubule bicarbonate reclamation    
gene <- "ENSMUSG00000004655"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

#Group plots for Aqp5, Aqp4, and Aqp1
gene_group <- c("ENSMUSG00000044217", "ENSMUSG00000024411", "ENSMUSG00000004655")
plotExpression(object = sce, features = gene_group, x = "celltype", colour_by ="celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 69057 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene_group, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

PIN6 Orthologs

##PIN6: auxin-activated signaling pathway    negative regulation of ethylene-activated signaling pathway     root hair elongation    transmembrane transport     negative regulation of lateral root development        
#Gpr155 ----  Flybase (1/9 YY)  
# intracellular signal transduction  cognition  transmembrane transport  
gene <- "ENSMUSG00000041762"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

plotExpression(object = sce, features = gene, x = "celltype", colour_by = "celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 23019 rows containing missing values (geom_point).

ABCB4 Orthologs

##ABCB4: gravitropism   response to auxin     response to cytokinin   xenobiotic transport   root hair elongation    transmembrane  ABC transporters             
#Abcb1a ----  Flybase (9/9 YY)  e!(41%, many to many, certainity: NO)
# placenta development   brain development   circadian rhythm    hormone transport   response to organic substance   maintenance of blood-brain barrier  MicroRNAs in cancer    ABC transporters         
gene <- "ENSMUSG00000040584"
plotReducedDim(object = sce, dimred = "umap", colour_by = gene)

Warning: Removed 23019 rows containing missing values (geom_point).

plotExpression(object = sce, features = gene, x = "stage", colour_by = "stage") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

plotExpression(object = sce, features = gene, x = "celltype", colour_by = "celltype") +
  theme(axis.text.x = element_text(angle = 90), legend.position = "none")

Warning: Removed 23019 rows containing missing values (geom_point).

sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8 (Core)

Matrix products: default
BLAS:   /home/idies/R/lib64/R/lib/libRblas.so
LAPACK: /home/idies/R/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] cowplot_1.1.1               scater_1.22.0              
 [3] ggplot2_3.3.5               scran_1.22.1               
 [5] scuttle_1.4.0               SingleCellExperiment_1.16.0
 [7] SummarizedExperiment_1.24.0 Biobase_2.54.0             
 [9] GenomicRanges_1.46.1        GenomeInfoDb_1.30.0        
[11] IRanges_2.28.0              S4Vectors_0.32.3           
[13] BiocGenerics_0.40.0         MatrixGenerics_1.6.0       
[15] matrixStats_0.61.0         

loaded via a namespace (and not attached):
 [1] bitops_1.0-7              tools_4.1.2               bslib_0.3.1              
 [4] utf8_1.2.2                R6_2.5.1                  irlba_2.3.5              
 [7] vipor_0.4.5               DBI_1.1.2                 colorspace_2.0-2         
[10] withr_2.4.3               tidyselect_1.1.1          gridExtra_2.3            
[13] compiler_4.1.2            BiocNeighbors_1.12.0      DelayedArray_0.20.0      
[16] sass_0.4.0                labeling_0.4.2            scales_1.1.1             
[19] stringr_1.4.0             digest_0.6.29             rmarkdown_2.11           
[22] XVector_0.34.0            pkgconfig_2.0.3           htmltools_0.5.2          
[25] sparseMatrixStats_1.6.0   fastmap_1.1.0             limma_3.50.0             
[28] rlang_0.4.12              DelayedMatrixStats_1.16.0 jquerylib_0.1.4          
[31] generics_0.1.1            farver_2.1.0              jsonlite_1.7.3           
[34] BiocParallel_1.28.3       dplyr_1.0.7               RCurl_1.98-1.5           
[37] magrittr_2.0.1            BiocSingular_1.10.0       GenomeInfoDbData_1.2.7   
[40] Matrix_1.3-4              Rcpp_1.0.8                ggbeeswarm_0.6.0         
[43] munsell_0.5.0             fansi_1.0.2               viridis_0.6.2            
[46] lifecycle_1.0.1           stringi_1.7.6             yaml_2.2.1               
[49] edgeR_3.36.0              zlibbioc_1.40.0           grid_4.1.2               
[52] parallel_4.1.2            ggrepel_0.9.1             dqrng_0.3.0              
[55] crayon_1.4.2              lattice_0.20-45           beachmat_2.10.0          
[58] locfit_1.5-9.4            metapod_1.2.0             knitr_1.37               
[61] pillar_1.6.4              igraph_1.2.11             ScaledMatrix_1.2.0       
[64] glue_1.6.0                evaluate_0.14             vctrs_0.3.8              
[67] gtable_0.3.0              purrr_0.3.4               assertthat_0.2.1         
[70] xfun_0.29                 rsvd_1.0.5                viridisLite_0.4.0        
[73] tibble_3.1.6              beeswarm_0.4.0            cluster_2.1.2            
[76] bluster_1.4.0             statmod_1.4.36            ellipsis_0.3.2