FGCZ banner

Started on 2017-09-05 15:21:03

TwoGroupsAnalysis_Result

Settings

Setting
Analysis: NGS two group analysis
Feature level: gene
Data Column Used: matchCounts
Method: deseq2
Comparison: Glyc_Eth–over–Glucose
Normalization: quantile
Differential expression test: QL
Log2 signal threshold: 3.322
Linear signal threshold: 10

Result Summary

Number
Number of features: 7126
Number of features with counts above threshold: 5615

Number of significants by p-value and fold-change

#significants FDR fc >= 1 fc >= 1.5 fc >= 2 fc >= 3 fc >= 4 fc >= 8 fc >= 10
p < 0.1 2549 0.2199000 2549 1632 793 394 269 110 90
p < 0.05 2133 0.1315000 2133 1533 765 390 269 110 90
p < 0.01 1505 0.0371400 1505 1289 722 382 268 110 90
p < 0.001 1019 0.0054300 1019 971 631 347 248 105 87
p < 1e-04 750 0.0007452 750 741 555 328 237 104 86
p < 1e-05 588 0.0000954 588 585 486 300 223 100 84

Full result table for opening with a spreadsheet program (e.g. Excel: when opening with Excel, make sure that the Gene symbols are loaded into a column formatted as ‘text’ that prevents conversion of the symbols to dates).

result–Glyc_Eth–over–Glucose.zip

Live Report and Visualizations

Inspection of significant genes

Inspection of significant genes (Advanced plots)

Plot in pdf

Interactive comparison plot (With thousands of genes, it can be slow and requires a modern web brwoser for best javascript performance!)

Intra-group Comparison: Glucose

Intra-group Comparison: Glyc_Eth

Clustering of Significant Features

Number
Significance threshold: 0.01
log2 Ratio threshold: 0.5
Number of significant features: 1408

Cluster Plot

GO categories of feature clusters
BP MF CC
Cluster 1 Cluster-BP-1.html Cluster-MF-1.html Cluster-CC-1.html
Cluster 2 Cluster-BP-2.html Cluster-MF-2.html Cluster-CC-2.html
Cluster 3 Cluster-BP-3.html Cluster-MF-3.html Cluster-CC-3.html
Cluster 4
Cluster 5 Cluster-BP-5.html Cluster-MF-5.html Cluster-CC-5.html
Cluster 6 Cluster-BP-6.html Cluster-MF-6.html Cluster-CC-6.html
a Cluster font color corresponds to the row colors in the heatmap plot.

Plot in pdf

GO cluster tables

Enrichr

GO Enrichment Analysis (goseq)

Maximum number of terms displayed: 40.

enrichUp enrichDown enrichBoth
BP Cluster-BP-enrichUp.html Cluster-BP-enrichDown.html Cluster-BP-enrichBoth.html
MF Cluster-MF-enrichUp.html Cluster-MF-enrichDown.html Cluster-MF-enrichBoth.html
CC Cluster-CC-enrichUp.html Cluster-CC-enrichDown.html Cluster-CC-enrichBoth.html
GO categories that are overrepresented among significantly upregulated genes.
Biological Proc. (BP) Molecular Func. (MF) Cellular Comp. (CC)
Term ID p N Term ID p N Term ID p N
biological_process GO:0008150 5.297847e-09 192/889 oxidoreductase activity GO:0016491 6.243565e-19 94/263 cellular_component GO:0005575 3.078621e-07 123/509
transmembrane transporter activity GO:0022857 7.196866e-11 82/282
GO categories that are overrepresented among significantly downregulated genes.
Biological Proc. (BP) Molecular Func. (MF) Cellular Comp. (CC)
Term ID p N Term ID p N Term ID p N
cytoplasmic translation GO:0002181 5.794296e-09 71/167 ligase activity GO:0016874 1.150735e-05 31/97 ribosome GO:0005840 8.716452e-08 98/345
translational elongation GO:0006414 1.234173e-05 21/44 structural constituent of ribosome GO:0003735 3.979891e-05 67/220
cellular amino acid metabolic process GO:0006520 4.925931e-05 52/203
GO categories that are overrepresented among all significantly regulated genes.
Biological Proc. (BP) Molecular Func. (MF) Cellular Comp. (CC)
Term ID p N Term ID p N Term ID p N
biological_process GO:0008150 1.004028e-07 273/889 oxidoreductase activity GO:0016491 1.780544e-12 132/263 cellular_component GO:0005575 1.82968e-07 164/509
transmembrane transporter activity GO:0022857 2.286259e-11 131/282
ligase activity GO:0016874 6.691161e-05 47/97

ReViGO

enrichUp enrichDown enrichBoth
BP ReViGO ReViGO ReViGO
MF ReViGO ReViGO ReViGO
CC ReViGO ReViGO ReViGO

Hypergeometric overrepresentation test

dotplot

enrichMap

cnetplot

Gene set enrichment analysis

dotplot

enrichMap

cnetplot

Input Dataset

SessionInfo

## R version 3.4.0 (2017-04-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 8 (jessie)
## 
## Matrix products: default
## BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
## LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
##  [3] LC_TIME=de_DE.UTF-8           LC_COLLATE=en_US.UTF-8       
##  [5] LC_MONETARY=de_DE.UTF-8       LC_MESSAGES=en_US.UTF-8      
##  [7] LC_PAPER=de_DE.UTF-8          LC_NAME=de_DE.UTF-8          
##  [9] LC_ADDRESS=de_DE.UTF-8        LC_TELEPHONE=de_DE.UTF-8     
## [11] LC_MEASUREMENT=de_DE.UTF-8    LC_IDENTIFICATION=de_DE.UTF-8
## 
## attached base packages:
##  [1] tools     stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] clusterProfiler_3.4.4      DOSE_3.2.0                
##  [3] GO.db_3.4.1                annotate_1.54.0           
##  [5] XML_3.98-1.7               GOstats_2.42.0            
##  [7] graph_1.54.0               Category_2.42.0           
##  [9] Matrix_1.2-10              AnnotationDbi_1.38.0      
## [11] gplots_3.0.1               ReporteRs_0.8.6           
## [13] ReporteRsjars_0.0.2        plotly_4.7.0              
## [15] ggplot2_2.2.1              htmltools_0.3.6           
## [17] DT_0.2                     htmlwidgets_0.8           
## [19] webshot_0.4.1              kableExtra_0.2.1          
## [21] knitr_1.16                 SummarizedExperiment_1.6.3
## [23] DelayedArray_0.2.4         matrixStats_0.52.2        
## [25] Biobase_2.36.2             ezRun_1.0.15              
## [27] GenomicRanges_1.28.3       GenomeInfoDb_1.12.0       
## [29] Biostrings_2.44.0          XVector_0.16.0            
## [31] IRanges_2.10.1             S4Vectors_0.14.1          
## [33] BiocGenerics_0.22.0        data.table_1.10.4         
## 
## loaded via a namespace (and not attached):
##   [1] fgsea_1.2.1              colorspace_1.3-2        
##   [3] rprojroot_1.2            qvalue_2.8.0            
##   [5] htmlTable_1.9            base64enc_0.1-3         
##   [7] xml2_1.1.1               splines_3.4.0           
##   [9] R.methodsS3_1.7.1        GOSemSim_2.2.0          
##  [11] geneplotter_1.54.0       Formula_1.2-1           
##  [13] jsonlite_1.4             Rsamtools_1.28.0        
##  [15] rJava_0.9-8              cluster_2.0.6           
##  [17] png_0.1-7                R.oo_1.21.0             
##  [19] geneLenDataBase_1.12.0   shiny_1.0.3             
##  [21] compiler_3.4.0           httr_1.2.1              
##  [23] rvcheck_0.0.9            backports_1.1.0         
##  [25] assertthat_0.2.0         lazyeval_0.2.0          
##  [27] acepack_1.4.1            igraph_1.0.1            
##  [29] gtable_0.2.0             glue_1.1.0              
##  [31] GenomeInfoDbData_0.99.0  reshape2_1.4.2          
##  [33] DO.db_2.9                dplyr_0.7.0             
##  [35] fastmatch_1.1-0          Rcpp_0.12.11            
##  [37] nlme_3.1-131             gdata_2.18.0            
##  [39] rtracklayer_1.36.3       crosstalk_1.0.0         
##  [41] stringr_1.2.0            rvest_0.3.2             
##  [43] mime_0.5                 gtools_3.5.0            
##  [45] zlibbioc_1.22.0          scales_0.4.1            
##  [47] RBGL_1.52.0              RColorBrewer_1.1-2      
##  [49] yaml_2.1.14              memoise_1.1.0           
##  [51] goseq_1.28.0             gridExtra_2.2.1         
##  [53] gdtools_0.1.4            biomaRt_2.32.0          
##  [55] rpart_4.1-11             latticeExtra_0.6-28     
##  [57] stringi_1.1.5            RSQLite_1.1-2           
##  [59] highr_0.6                genefilter_1.58.1       
##  [61] checkmate_1.8.2          GenomicFeatures_1.28.1  
##  [63] caTools_1.17.1           zip_1.0.0               
##  [65] BiocParallel_1.10.1      rlang_0.1.1             
##  [67] bitops_1.0-6             evaluate_0.10           
##  [69] lattice_0.20-35          purrr_0.2.2.2           
##  [71] labeling_0.3             GenomicAlignments_1.12.1
##  [73] rvg_0.1.3                GSEABase_1.38.0         
##  [75] AnnotationForge_1.18.0   plyr_1.8.4              
##  [77] magrittr_1.5             DESeq2_1.16.1           
##  [79] R6_2.2.1                 Hmisc_4.0-3             
##  [81] DBI_0.6-1                mgcv_1.8-17             
##  [83] foreign_0.8-68           survival_2.41-3         
##  [85] RCurl_1.95-4.8           nnet_7.3-12             
##  [87] tibble_1.3.3             uuid_0.1-2              
##  [89] KernSmooth_2.23-15       rmarkdown_1.5           
##  [91] officer_0.1.3            locfit_1.5-9.1          
##  [93] grid_3.4.0               digest_0.6.12           
##  [95] xtable_1.8-2             tidyr_0.6.3             
##  [97] httpuv_1.3.3             R.utils_2.5.0           
##  [99] munsell_0.4.3            viridisLite_0.2.0       
## [101] BiasedUrn_1.07