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 3.4.4 (2018-03-15)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.4 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    methods   stats     graphics  grDevices utils    
## [8] datasets  base     
## 
## other attached packages:
##  [1] bindrcpp_0.2.2       transite_0.99.3      DT_0.4              
##  [4] knitr_1.20           AnnotationDbi_1.40.0 IRanges_2.12.0      
##  [7] S4Vectors_0.16.0     Biobase_2.38.0       BiocGenerics_0.24.0 
## [10] rmarkdown_1.9        futile.logger_1.4.3 
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.3.1                             
##  [2] RMySQL_0.10.15                         
##  [3] jsonlite_1.5                           
##  [4] bit64_0.9-7                            
##  [5] shiny_1.1.0                            
##  [6] assertthat_0.2.0                       
##  [7] blob_1.1.1                             
##  [8] GenomeInfoDbData_1.0.0                 
##  [9] Rsamtools_1.30.0                       
## [10] yaml_2.1.19                            
## [11] progress_1.1.2                         
## [12] lattice_0.20-35                        
## [13] pillar_1.2.3                           
## [14] RSQLite_2.1.1                          
## [15] backports_1.1.2                        
## [16] glue_1.2.0                             
## [17] digest_0.6.15                          
## [18] promises_1.0.1                         
## [19] RColorBrewer_1.1-2                     
## [20] GenomicRanges_1.30.3                   
## [21] XVector_0.18.0                         
## [22] colorspace_1.3-2                       
## [23] httpuv_1.4.3                           
## [24] htmltools_0.3.6                        
## [25] Matrix_1.2-14                          
## [26] plyr_1.8.4                             
## [27] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0
## [28] XML_3.98-1.11                          
## [29] pkgconfig_2.0.1                        
## [30] biomaRt_2.34.2                         
## [31] zlibbioc_1.24.0                        
## [32] xtable_1.8-2                           
## [33] purrr_0.2.5                            
## [34] scales_0.5.0                           
## [35] later_0.7.2                            
## [36] BiocParallel_1.12.0                    
## [37] tibble_1.4.2                           
## [38] ggplot2_2.2.1                          
## [39] SummarizedExperiment_1.8.1             
## [40] GenomicFeatures_1.30.3                 
## [41] TFMPvalue_0.0.8                        
## [42] lazyeval_0.2.1                         
## [43] mime_0.5                               
## [44] magrittr_1.5                           
## [45] memoise_1.1.0                          
## [46] evaluate_0.10.1                        
## [47] tools_3.4.4                            
## [48] prettyunits_1.0.2                      
## [49] org.Hs.eg.db_3.5.0                     
## [50] formatR_1.5                            
## [51] matrixStats_0.53.1                     
## [52] stringr_1.3.1                          
## [53] munsell_0.4.3                          
## [54] DelayedArray_0.4.1                     
## [55] lambda.r_1.2.3                         
## [56] Biostrings_2.46.0                      
## [57] compiler_3.4.4                         
## [58] GenomeInfoDb_1.14.0                    
## [59] rlang_0.2.1                            
## [60] grid_3.4.4                             
## [61] RCurl_1.95-4.10                        
## [62] htmlwidgets_1.2                        
## [63] crosstalk_1.0.0                        
## [64] labeling_0.3                           
## [65] bitops_1.0-6                           
## [66] gtable_0.2.0                           
## [67] DBI_1.0.0                              
## [68] R6_2.2.2                               
## [69] GenomicAlignments_1.14.2               
## [70] gridExtra_2.3                          
## [71] dplyr_0.7.5                            
## [72] rtracklayer_1.38.3                     
## [73] bit_1.1-14                             
## [74] bindr_0.1.1                            
## [75] rprojroot_1.3-2                        
## [76] futile.options_1.0.1                   
## [77] stringi_1.2.2                          
## [78] Rcpp_0.12.17                           
## [79] dbplyr_1.2.1                           
## [80] tidyselect_0.2.4