Reactome

Visualisation

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Last updated: 2024-01-13

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Knit directory: 4_Treg_uNK/1_analysis/

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Unstaged changes:
    Modified:   0_data/rds_objects/comp.rds
    Modified:   0_data/rds_objects/dge.rds
    Modified:   0_data/rds_objects/enrichGO.rds
    Modified:   0_data/rds_objects/enrichGO_sig.rds
    Modified:   0_data/rds_objects/enrichKEGG.rds
    Modified:   0_data/rds_objects/enrichKEGG_all.rds
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    Modified:   3_output/de_genes_all.xlsx
    Modified:   3_output/de_genes_sig.xlsx
    Modified:   3_output/reactome_all.xlsx
    Modified:   3_output/reactome_sig.xlsx

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File	Version	Author	Date	Message
Rmd	a957cff	Ha Manh Tran	2024-01-13	workflowr::wflow_publish(here::here("1_analysis/*Rmd"))
Rmd	c78dfac	tranmanhha135	2024-01-12	remote from ipad
Rmd	221e2fa	tranmanhha135	2024-01-10	fixed error
Rmd	7d64f82	tranmanhha135	2024-01-09	completed ORA GO
Rmd	05fa0b3	tranmanhha135	2024-01-06	added description

# working with data
library(dplyr)
library(magrittr)
library(readr)
library(tibble)
library(reshape2)
library(tidyverse)

# Visualisation:
library(kableExtra)
library(ggplot2)
library(grid)
library(pander)
library(cowplot)
library(pheatmap)
library(DT)
library(extrafont)
# Custom ggplot
library(ggbiplot)
library(ggrepel)

# Bioconductor packages:
library(edgeR)
library(limma)
library(Glimma)
library(clusterProfiler)
library(org.Mm.eg.db)
library(enrichplot)
library(ReactomePA)
library(pandoc)
library(knitr)
opts_knit$set(progress = FALSE, verbose = FALSE)
opts_chunk$set(warning=FALSE, message=FALSE, echo=FALSE)

Reactome

Reactome database provides curated information about biological pathways, including molecular events and reactions within cells. It focuses on human biology and is widely used for pathway analysis and functional interpretation of high-throughput data.

KEGG and Reactome both include approximately the same number of genes. The difference lies in KEGG’s use of broader terms, while Reactome employs similar terms but with multiple detailed entries.

In the Reactome database, terms are organized hierarchically based on the classification of biological pathways. The organization follows a tree-like structure, where terms represent different levels of granularity in understanding molecular events and reactions within cells

Visualisation

The following visualisations are Reactome enrichment analysis performed with set of DE genes significantly below FDR < 0.1 without FC threshold (TREAT). IMPORTANTLY, significant Reactome pathways are significantly if FDR < 0.1

Dot plot: illustrates the enriched Reactome pathways
- $Gene ratio =$ the number of significant DE gene in the term / the total of number of genes in the term as indicated by the size
Table: list of all the significant Reactome pathways
Upset: illustrate the overlap of gene between different pathways

I recommend reading through the full list of significant Reactome pathways and selecting the most biologically relevant for more in-depth visualisation

Show entries

Search:

	Description	GeneRatio	pvalue	p.adjust	logFDR	qvalue	geneID	Count
R-MMU-1236974	ER-Phagosome pathway	0.375	6.98e-06	0.00395	2.4	0.00381	H2-Q4/Tap1/B2m/H2-K1/Tap2/H2-T23	6
R-MMU-983170	Antigen Presentation: Folding, assembly and peptide loading of class I MHC	0.261	7.26e-05	0.0174	1.76	0.0168	H2-Q4/Tap1/B2m/H2-K1/Tap2/H2-T23	6
R-MMU-1236975	Antigen processing-Cross presentation	0.141	9.22e-05	0.0174	1.76	0.0168	H2-Q4/Tap1/B2m/H2-K1/Tap2/Psmb8/Psmb9/H2-T23/Psme1/Psme2	10
R-MMU-1474244	Extracellular matrix organization	0.0904	0.000206	0.0291	1.54	0.0281	Lox/Tgfb2/Col24a1/Col4a6/Col4a5/Loxl3/Ctsg/Adam8/Col7a1/Ctsk/Icam1/Cdh1/Mmp15/Mfap4/Colgalt2/Mmp14	16
R-MMU-977606	Regulation of Complement cascade	0.263	0.000286	0.0324	1.49	0.0313	C2/Serping1/Clu/Cd55/C1ra	5
R-MMU-1474228	Degradation of the extracellular matrix	0.125	0.000517	0.0447	1.35	0.0432	Col4a6/Col4a5/Ctsg/Adam8/Col7a1/Ctsk/Cdh1/Mmp15/Mmp14	9
R-MMU-166658	Complement cascade	0.227	0.000598	0.0447	1.35	0.0432	C2/Serping1/Clu/Cd55/C1ra	5
R-MMU-1592389	Activation of Matrix Metalloproteinases	0.308	0.000632	0.0447	1.35	0.0432	Ctsg/Ctsk/Mmp15/Mmp14	4
R-MMU-1442490	Collagen degradation	0.171	0.00084	0.0488	1.31	0.0471	Col4a6/Col4a5/Col7a1/Ctsk/Mmp15/Mmp14	6
R-MMU-2243919	Crosslinking of collagen fibrils	0.286	0.000862	0.0488	1.31	0.0471	Lox/Col4a6/Col4a5/Loxl3	4

Showing 1 to 10 of 13 entries

Previous1 2Next

Show entries

Search:

	Description	GeneRatio	pvalue	p.adjust	logFDR	qvalue	geneID	Count
R-MMU-6809371	Formation of the cornified envelope	0.4	1.48e-07	7.45e-05	4.13	7.36e-05	Krt18/Krt7/Krt8/Krt19/Ppl/Pkp4/Krt17/Krt80/Perp/Krt84	10
R-MMU-6805567	Keratinization	0.385	2.3e-07	7.45e-05	4.13	7.36e-05	Krt18/Krt7/Krt8/Krt19/Ppl/Pkp4/Krt17/Krt80/Perp/Krt84	10

Showing 1 to 2 of 2 entries

Previous1Next

Show entries

Search:

	Description	GeneRatio	pvalue	p.adjust	logFDR	qvalue	geneID	Count
R-MMU-1236974	ER-Phagosome pathway	0.188	0.000238	0.0542	1.27	0.0516	H2-K1/B2m/H2-T23	3
R-MMU-983170	Antigen Presentation: Folding, assembly and peptide loading of class I MHC	0.13	0.000723	0.0595	1.23	0.0566	H2-K1/B2m/H2-T23	3
R-MMU-6809371	Formation of the cornified envelope	0.12	0.000929	0.0595	1.23	0.0566	Krt84/Krt18/Dsc2	3
R-MMU-6805567	Keratinization	0.115	0.00104	0.0595	1.23	0.0566	Krt84/Krt18/Dsc2	3
R-MMU-176408	Regulation of APC/C activators between G1/S and early anaphase	0.0909	0.00211	0.0815	1.09	0.0775	Cdc23/Plk1/Bub1b	3
R-MMU-1474228	Degradation of the extracellular matrix	0.0556	0.00234	0.0815	1.09	0.0775	Eln/Spp1/Adam8/Adamts4	4
R-MMU-2172127	DAP12 interactions	0.0857	0.0025	0.0815	1.09	0.0775	H2-K1/B2m/H2-T23	3
R-MMU-2299718	Condensation of Prophase Chromosomes	0.182	0.00318	0.0905	1.04	0.0861	Ncapd3/Plk1	2

Showing 1 to 8 of 8 entries

Previous1Next

Export Data

The following are exported:

reactome_all.xlsx - This spreadsheet contains all Reactome pathways
reactome_sig.xlsx - This spreadsheet contains all significant (FDR < 0.1) Reactome pathways

R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_Australia.utf8  LC_CTYPE=English_Australia.utf8   
[3] LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.utf8    

time zone: Australia/Adelaide
tzcode source: internal

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

other attached packages:
 [1] knitr_1.45            pandoc_0.2.0          ReactomePA_1.44.0    
 [4] enrichplot_1.20.3     org.Mm.eg.db_3.17.0   AnnotationDbi_1.62.2 
 [7] IRanges_2.34.1        S4Vectors_0.38.2      Biobase_2.60.0       
[10] BiocGenerics_0.46.0   clusterProfiler_4.8.3 Glimma_2.10.0        
[13] edgeR_3.42.4          limma_3.56.2          ggrepel_0.9.4        
[16] ggbiplot_0.55         scales_1.3.0          plyr_1.8.9           
[19] extrafont_0.19        DT_0.31               pheatmap_1.0.12      
[22] cowplot_1.1.2         pander_0.6.5          kableExtra_1.3.4     
[25] lubridate_1.9.3       forcats_1.0.0         stringr_1.5.1        
[28] purrr_1.0.2           tidyr_1.3.0           ggplot2_3.4.4        
[31] tidyverse_2.0.0       reshape2_1.4.4        tibble_3.2.1         
[34] readr_2.1.4           magrittr_2.0.3        dplyr_1.1.4          

loaded via a namespace (and not attached):
  [1] splines_4.3.1               later_1.3.2                
  [3] bitops_1.0-7                ggplotify_0.1.2            
  [5] polyclip_1.10-6             graph_1.78.0               
  [7] lifecycle_1.0.4             rprojroot_2.0.4            
  [9] lattice_0.21-8              MASS_7.3-60                
 [11] crosstalk_1.2.1             sass_0.4.8                 
 [13] rmarkdown_2.25              jquerylib_0.1.4            
 [15] yaml_2.3.7                  httpuv_1.6.13              
 [17] DBI_1.2.0                   RColorBrewer_1.1-3         
 [19] abind_1.4-5                 zlibbioc_1.46.0            
 [21] rvest_1.0.3                 GenomicRanges_1.52.1       
 [23] ggraph_2.1.0                RCurl_1.98-1.13            
 [25] yulab.utils_0.1.1           tweenr_2.0.2               
 [27] rappdirs_0.3.3              git2r_0.33.0               
 [29] GenomeInfoDbData_1.2.10     tidytree_0.4.6             
 [31] reactome.db_1.84.0          svglite_2.1.3              
 [33] codetools_0.2-19            DelayedArray_0.26.7        
 [35] DOSE_3.26.2                 xml2_1.3.6                 
 [37] ggforce_0.4.1               tidyselect_1.2.0           
 [39] aplot_0.2.2                 farver_2.1.1               
 [41] viridis_0.6.4               matrixStats_1.2.0          
 [43] webshot_0.5.5               jsonlite_1.8.8             
 [45] ellipsis_0.3.2              tidygraph_1.3.0            
 [47] systemfonts_1.0.5           tools_4.3.1                
 [49] treeio_1.24.3               Rcpp_1.0.11                
 [51] glue_1.6.2                  gridExtra_2.3              
 [53] Rttf2pt1_1.3.12             here_1.0.1                 
 [55] xfun_0.39                   DESeq2_1.40.2              
 [57] qvalue_2.32.0               MatrixGenerics_1.12.3      
 [59] GenomeInfoDb_1.36.4         withr_2.5.2                
 [61] fastmap_1.1.1               fansi_1.0.6                
 [63] digest_0.6.33               timechange_0.2.0           
 [65] R6_2.5.1                    gridGraphics_0.5-1         
 [67] colorspace_2.1-0            GO.db_3.17.0               
 [69] RSQLite_2.3.4               utf8_1.2.4                 
 [71] generics_0.1.3              data.table_1.14.10         
 [73] graphlayouts_1.0.2          httr_1.4.7                 
 [75] htmlwidgets_1.6.4           S4Arrays_1.0.6             
 [77] scatterpie_0.2.1            graphite_1.46.0            
 [79] whisker_0.4.1               pkgconfig_2.0.3            
 [81] gtable_0.3.4                blob_1.2.4                 
 [83] workflowr_1.7.1             XVector_0.40.0             
 [85] shadowtext_0.1.2            htmltools_0.5.7            
 [87] fgsea_1.26.0                ggupset_0.3.0              
 [89] png_0.1-8                   ggfun_0.1.3                
 [91] rstudioapi_0.15.0           tzdb_0.4.0                 
 [93] nlme_3.1-164                cachem_1.0.8               
 [95] parallel_4.3.1              HDO.db_0.99.1              
 [97] pillar_1.9.0                vctrs_0.6.5                
 [99] promises_1.2.1              extrafontdb_1.0            
[101] evaluate_0.23               cli_3.6.1                  
[103] locfit_1.5-9.8              compiler_4.3.1             
[105] rlang_1.1.1                 crayon_1.5.2               
[107] labeling_0.4.3              fs_1.6.3                   
[109] stringi_1.8.3               viridisLite_0.4.2          
[111] BiocParallel_1.34.2         munsell_0.5.0              
[113] Biostrings_2.68.1           lazyeval_0.2.2             
[115] GOSemSim_2.26.1             Matrix_1.6-4               
[117] hms_1.1.3                   patchwork_1.1.3            
[119] bit64_4.0.5                 KEGGREST_1.40.1            
[121] highr_0.10                  SummarizedExperiment_1.30.2
[123] igraph_1.6.0                memoise_2.0.1              
[125] bslib_0.6.1                 ggtree_3.8.2               
[127] fastmatch_1.1-4             bit_4.0.5                  
[129] downloader_0.4              ape_5.7-1                  
[131] gson_0.1.0

Reactome analysis

Ha M. Tran

12-01-2024

Reactome

Visualisation

Export Data