1.1 Configuration

Analysis approach:

approach <- "kmer"

Species:

species <- "human"

Graphical output format:

graphics.format <- "SVG"

Sequence region:

sequence.type <- "3UTR"

P-value adjustment method:

p.adjust.method <- "BH"

P-value combining method:

p.combining.method <- "SL"

k-mer length:

k <- 6

Significance threshold for k-mers:

kmer.significance.threshold <- 0.01

Motif database:

motif.db <- "transite"

1.2 Sequence data retrieval

• retrieve requested sequence regions (3’ UTRs, 5’ UTRs, or mature mRNAs) for each RefSeq identifier using
  • GRCh38/hg38 genome assembly for human platforms
  • GRCm38/mm10 genome assembly for mouse platforms
• draw histogram of length distribution of retrieved sequences

The latest genome assembly releases (GRCh38/hg38 for human platforms, GRCm38/mm10 for mouse platforms) are used to retrieve the requested sequence regions for all specified transcripts.

Sequence data retrieval summary:

Length distribution of retrieved sequences:

4.1 Loaded motifs

4.2 R Session info

## R version 3.5.1 (2018-07-02)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.5 LTS
## 
## Matrix products: default
## BLAS: /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
## 
## 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] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] bindrcpp_0.2.2       transite_0.99.3      DT_0.4              
##  [4] knitr_1.20           AnnotationDbi_1.42.1 IRanges_2.14.11     
##  [7] S4Vectors_0.18.3     Biobase_2.40.0       BiocGenerics_0.26.0 
## [10] rmarkdown_1.10       futile.logger_1.4.3 
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.3.1                             
##  [2] jsonlite_1.5                           
##  [3] bit64_0.9-7                            
##  [4] shiny_1.1.0                            
##  [5] assertthat_0.2.0                       
##  [6] blob_1.1.1                             
##  [7] GenomeInfoDbData_1.1.0                 
##  [8] Rsamtools_1.32.3                       
##  [9] yaml_2.2.0                             
## [10] progress_1.2.0                         
## [11] lattice_0.20-35                        
## [12] pillar_1.3.0                           
## [13] RSQLite_2.1.1                          
## [14] backports_1.1.2                        
## [15] glue_1.3.0                             
## [16] digest_0.6.17                          
## [17] promises_1.0.1                         
## [18] RColorBrewer_1.1-2                     
## [19] GenomicRanges_1.32.6                   
## [20] XVector_0.20.0                         
## [21] colorspace_1.3-2                       
## [22] httpuv_1.4.5                           
## [23] Matrix_1.2-14                          
## [24] htmltools_0.3.6                        
## [25] plyr_1.8.4                             
## [26] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0
## [27] XML_3.98-1.16                          
## [28] pkgconfig_2.0.2                        
## [29] biomaRt_2.36.1                         
## [30] zlibbioc_1.26.0                        
## [31] xtable_1.8-3                           
## [32] purrr_0.2.5                            
## [33] scales_1.0.0                           
## [34] later_0.7.4                            
## [35] BiocParallel_1.14.2                    
## [36] tibble_1.4.2                           
## [37] ggplot2_3.0.0                          
## [38] SummarizedExperiment_1.10.1            
## [39] GenomicFeatures_1.32.2                 
## [40] TFMPvalue_0.0.8                        
## [41] lazyeval_0.2.1                         
## [42] mime_0.5                               
## [43] magrittr_1.5                           
## [44] crayon_1.3.4                           
## [45] memoise_1.1.0                          
## [46] evaluate_0.11                          
## [47] tools_3.5.1                            
## [48] prettyunits_1.0.2                      
## [49] hms_0.4.2                              
## [50] org.Hs.eg.db_3.6.0                     
## [51] matrixStats_0.54.0                     
## [52] formatR_1.5                            
## [53] stringr_1.3.1                          
## [54] munsell_0.5.0                          
## [55] DelayedArray_0.6.6                     
## [56] lambda.r_1.2.3                         
## [57] Biostrings_2.48.0                      
## [58] compiler_3.5.1                         
## [59] GenomeInfoDb_1.16.0                    
## [60] rlang_0.2.2                            
## [61] grid_3.5.1                             
## [62] RCurl_1.95-4.11                        
## [63] htmlwidgets_1.2                        
## [64] crosstalk_1.0.0                        
## [65] labeling_0.3                           
## [66] bitops_1.0-6                           
## [67] gtable_0.2.0                           
## [68] DBI_1.0.0                              
## [69] R6_2.2.2                               
## [70] GenomicAlignments_1.16.0               
## [71] gridExtra_2.3                          
## [72] dplyr_0.7.6                            
## [73] rtracklayer_1.40.6                     
## [74] bit_1.1-14                             
## [75] bindr_0.1.1                            
## [76] rprojroot_1.3-2                        
## [77] futile.options_1.0.1                   
## [78] stringi_1.2.4                          
## [79] Rcpp_0.12.18                           
## [80] dbplyr_1.2.2                           
## [81] tidyselect_0.2.4