Functional enrichment practical
DUBii 2021
Olivier Sand and Jacques van Helden
2021-03-29
Goal of this practical
This practical aims at showing how to analyze functional enrichment on a list of genes with gProfiler.
Study case : The Cancer Gene Atlas (TCGA) Breast Invasive Cancer (BIC) data
Description : https://du-bii.github.io/study-cases/Homo_sapiens/TCGA_study-case/
References
Load (clusters of differentially) expressed genes
First, you need to load the gene list, which can be found on the github repository, in the following file.
- 1000 top DEG genes: https://raw.githubusercontent.com/DU-Bii/module-3-Stat-R/master/stat-R_2021/data/TCGA_BIC_subset/BIC_edgeR_DEG_top_1000_geneIDs.txt
#### Load the gene list ####
message("Loading gene list")
## URL of the data folder on github
data_folder_url <- 'https://raw.githubusercontent.com/DU-Bii/module-3-Stat-R/master/stat-R_2021/data/TCGA_BIC_subset/'
gene_list_file <- "BIC_edgeR_DEG_top_1000_geneIDs.txt"
## Trick : the file is read as a one-column table, and we transform it to a vector with unlist()
gene_list <- unlist(read.delim(file = file.path(data_folder_url, gene_list_file), header = FALSE))
## Check the length of the gene list
length(gene_list)[1] 1000Gene list functional enrichment analysis with gost
- Use the
gost()function to get the enrichment results.
- Note: we use FDR as multiple testing correction.
#### Run enrichment analysis with gost() ####
message("Running the enrichment analysis")
## Run the analysis
gostres <- gost(query = gene_list,
organism = "hsapiens",
ordered_query = FALSE,
multi_query = FALSE,
significant = TRUE,
exclude_iea = FALSE,
measure_underrepresentation = FALSE,
evcodes = FALSE,
user_threshold = 0.05,
correction_method = "fdr",
domain_scope = "annotated",
custom_bg = NULL,
numeric_ns = "",
sources = NULL,
as_short_link = FALSE)
## Check the structure of the result
names(gostres)[1] "result" "meta" names(gostres$result) [1] "query" "significant" "p_value" "term_size" "query_size" "intersection_size" "precision" "recall" "term_id" "source" "term_name" "effective_domain_size"
[13] "source_order" "parents" kable(summary(gostres))| Length | Class | Mode | |
|---|---|---|---|
| result | 14 | data.frame | list |
| meta | 5 | -none- | list |
## Check the most significant results, formating for kable
#head(gostres$result)
kable(head(gostres$result), digits = c(0, 0, 15, 7, 7, 7, 3, 3, 0, 0, 7, 7, 0, 0))| query | significant | p_value | term_size | query_size | intersection_size | precision | recall | term_id | source | term_name | effective_domain_size | source_order | parents |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| query_1 | TRUE | 0.000000001366740 | 6767 | 941 | 459 | 0.488 | 0.068 | GO:0071840 | GO:BP | cellular component organization or biogenesis | 18092 | 19843 | GO:0009987 |
| query_1 | TRUE | 0.000000006547855 | 6576 | 941 | 444 | 0.472 | 0.068 | GO:0016043 | GO:BP | cellular component organization | 18092 | 5674 | GO:0071840 |
| query_1 | TRUE | 0.000001767254615 | 3562 | 941 | 260 | 0.276 | 0.073 | GO:0051641 | GO:BP | cellular localization | 18092 | 16066 | GO:0009987, GO:0051179 |
| query_1 | TRUE | 0.000001767254615 | 10855 | 941 | 652 | 0.693 | 0.060 | GO:0044237 | GO:BP | cellular metabolic process | 18092 | 12740 | GO:0008152, GO:0009987 |
| query_1 | TRUE | 0.000024193272382 | 6466 | 941 | 417 | 0.443 | 0.064 | GO:0048518 | GO:BP | positive regulation of biological process | 18092 | 14903 | GO:0008150, GO:0050789 |
| query_1 | TRUE | 0.000032046960665 | 2789 | 941 | 207 | 0.220 | 0.074 | GO:0008104 | GO:BP | protein localization | 18092 | 3549 | GO:0033036 |
# kable(head(gostres$result),
# format = c("%s", "%s", "%e", "%d", "%d", "%d", "%.3f", "%.3f", "%s", "%s", "%d", "%d", "%s", "%s"))
names(gostres$meta)[1] "query_metadata" "result_metadata" "genes_metadata" "timestamp" "version" - Visualize the results as an interactive plot
### Visualization ###
message("Generating a dynamic plot of the results")
# Plot the results
gostplot(gostres, capped = TRUE,
interactive = TRUE)Dynamic figure of the enrichment analysis.
We can now tune the parameters to get some additional information about the evidence code and the list of genes at the intersection between the query set and the functional classes. Note that this generates a table with very large columns.
### With the input gene IDs that intersect with the corresponding functional term ###
message("Running the enrichment analysis showing the intersections")
# With intersection (can be time consuming)
gostres2 <- gost(query = gene_list,
organism = "hsapiens",
ordered_query = FALSE,
multi_query = FALSE,
significant = TRUE,
exclude_iea = FALSE,
measure_underrepresentation = FALSE,
evcodes = TRUE,
user_threshold = 0.05,
correction_method = "fdr",
domain_scope = "annotated",
custom_bg = NULL,
numeric_ns = "", sources = NULL)
kable(head(gostres2$result), digits = c(0, 0, 15, 7, 7, 7, 3, 3, 0, 0, 7, 7, 0, 0, 0, 0))| query | significant | p_value | term_size | query_size | intersection_size | precision | recall | term_id | source | term_name | effective_domain_size | source_order | parents | evidence_codes | intersection |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| query_1 | TRUE | 0.000000001366740 | 6767 | 941 | 459 | 0.488 | 0.068 | GO:0071840 | GO:BP | cellular component organization or biogenesis | 18092 | 19843 | GO:0009987 | IEA,IMP IBA,IBA TAS IEA,IDA ISS IBA IEA,IEA,IDA IMP IBA TAS IEA,IDA IBA IEA,IMP,TAS,ISS IEA,IDA IGI IEP NAS IEA,ISS IEA,IMP IBA TAS,IDA,ISS IEA,IEA,ISS IBA IEA,IEA,ISS IEA,IDA IMP ISS IEA,IDA IBA IEA,IEA,IMP TAS,IMP ISS IBA IEA,NAS,IMP IBA,IDA IBA,ISS TAS IEA,IDA IMP NAS,TAS,IMP,IDA,IBA,IDA IMP IBA,IEA,IBA IEA,TAS,IDA IMP IBA IEA,IDA IBA TAS IEA,IMP,IMP,TAS,IDA IMP IBA IEA,IMP IEA,ISS IEA,TAS,ISS TAS IEA,IDA ISS IBA IEA,TAS IEA,IMP IGI ISS TAS,IDA TAS,IDA IMP IBA IEA,IDA IEA,IEA,IDA,ISS IEA,IMP,IMP IEA,IDA IMP IEA,IMP IBA,ISS IBA IEA,IMP ISS IBA IEA,IEA,IBA,IMP IGI IEP IBA TAS IEA,IMP ISS IBA TAS IEA,IBA,IBA TAS IEA,ISS IEA,IEA,IBA,IBA IEA,IEA,IMP,IMP IBA TAS IEA,IMP IBA IC IEA,IMP,IEA,ISS IBA IEA,IDA IMP ISS IBA IEA,IEP,IEA,IEA,ISS,IBA,IBA,IBA,IDA IEA,ISS TAS IEA,IEA,IBA,IMP,NAS,IDA TAS IEA,IBA TAS NAS,IDA IMP ISS IBA IEA,IDA,IDA ISS TAS IEA,IDA IMP IBA NAS IEA,ISS IBA IEA,IEA,IMP ISS IEA,TAS,IGI TAS,IEA,ISS TAS IEA,TAS,NAS,IMP ISS IBA TAS IEA,TAS,IMP,IEA,TAS IEA,IMP IBA IEA,ISS IEA,TAS,IMP,IMP IBA TAS,IGI TAS,IEA,IMP,IMP ISS IBA IEA,IMP,IDA IBA NAS IEA,IMP ISS TAS IEA,IDA,IBA TAS,IEA,IEA,IPI IMP IBA IEA,IBA,IDA IBA,IDA IMP IBA IEA,IMP IBA IEA,IDA,TAS,TAS,IBA,IMP,IBA,IEA,IDA IMP IGI TAS IEA,IDA IMP IGI IBA TAS IEA,IMP,IMP,IDA IGI ISS,ISS IBA,IEA,TAS,IMP IGI IBA,IDA IEA,IMP IEA,ISS IEA,IDA IEA,IMP IBA,ISS IBA IEA,IDA TAS,IMP IBA TAS IEA,IDA IMP IBA TAS IEA,TAS IEA,IEA,IDA,IMP,IEA,IDA TAS,IBA IEA,TAS,IEA,IDA IBA,IEA,IEA,ISS IBA IEA,ISS IBA IEA,IDA IBA IEA,IMP,IMP,ISS IBA IEA,IMP IBA,ISS IEA,IEA,TAS,IMP TAS,IBA TAS,IMP,IMP,ISS IEA,IEA,IDA,IEA,IBA TAS IEA,TAS,ISS IBA,IDA IGI TAS IEA,IDA IMP ISS,TAS,IEA,ISS IBA TAS IEA,IEA,TAS,TAS,IEA,IBA IEA,TAS,IMP IBA IEA,IBA TAS,IBA IEA,IMP ISS IEA,TAS,TAS,TAS,IDA ISS IEA,IMP IEA,IBA,IBA IEA,IBA,IBA,TAS,IMP IEA,TAS,IMP IBA IEA,ISS IEA,IMP IBA TAS IEA,IMP IBA TAS IEA,IMP IBA,TAS NAS,IMP,IMP IBA IEA,ISS TAS IEA,IMP IBA,IBA,IMP,TAS IEA,IDA IBA,IBA IEA,IBA TAS NAS IEA,TAS,IDA IBA IEA,IMP IGI ISS IEA,TAS NAS IEA,IMP IBA,IDA IMP ISS IBA,ISS IEA,IMP,IDA IBA TAS IEA,ISS IBA TAS IEA,IMP IBA,IEA,TAS,IMP IBA,IDA ISS IBA NAS IEA,IMP NAS IEA,IMP IGI ISS IBA,IDA IEA,IBA,ISS TAS IEA,TAS,IDA TAS IEA,IMP IBA,IDA IBA IEA,IBA TAS,IEA,IBA,IBA TAS IEA,TAS IEA,TAS IEA,IBA NAS IEA,IDA ISS IBA NAS,IMP IGI NAS IEA,IEA,IBA IEA,IMP IEA,IDA IBA IEA,TAS,IEA,IBA,IDA IBA TAS,IMP,IDA IMP ISS IBA TAS IEA,IDA IEA,TAS,IDA IEA,IMP,IBA,IDA IEA,IMP IBA IEA,IBA IEA,IEA,IBA TAS,IBA IEA,TAS,IMP,IEA,IMP IBA TAS IEA,IEA,IEA,IEA,IBA NAS IEA,TAS IEA,TAS,IEA,ISS IEA,IDA IMP HMP ISS IEA,IDA IEA,IEA,TAS,TAS,NAS,IDA,IMP,IMP IBA,ISS IBA IEA,IBA,IBA NAS IEA,IBA TAS,IMP,IMP,ISS IEA,ISS TAS,IDA IMP IEA,IDA IMP IBA IEA,IMP IBA IEA,IEA,IEA,IMP IEA,NAS,IBA NAS IEA,TAS,IEA,IBA IEA,IEA,IBA,IDA IMP ISS IBA,TAS,IBA IEA,IDA,TAS,TAS,IBA IEA,IMP IBA IEA,IMP IBA,TAS,IBA IEA,IDA ISS IEA,TAS,ISS TAS,IMP IBA,IMP,TAS,IMP IBA IEA,IMP,IEA,TAS IEA,TAS,ISS IBA TAS IEA,IDA IBA IEA,TAS IEA,IDA ISS,IDA,IDA IBA TAS,IEA,IBA,IBA IC IEA,TAS,IEA,IBA TAS,IMP IEA,IBA TAS,IDA IBA,ISS IBA IEA,IMP TAS,IMP,IDA IMP,TAS,TAS,TAS,IDA,IEA,IDA IMP IBA IEA,IDA IMP IBA IEA,ISS,IMP IEA,IMP,IMP,IMP IBA IEA,ISS,ISS IBA IEA,TAS,ISS IEA,IBA IEA,IMP IEA,ISS IBA,IBA TAS IEA,IMP ISS,IBA,IMP,IEA,IBA,ISS TAS IEA,IBA,IMP,IDA,IBA IEA,IDA IMP IBA TAS IEA,IBA,IMP IEA,IDA TAS IEA,IMP,IDA IMP IGI ISS IBA TAS IEA,TAS,IDA,IDA IMP IEA,IEA,ISS IEA,IMP IBA,IDA IEA,IBA IEA,IDA IMP IBA,IBA NAS IEA,IMP,IDA IMP IGI TAS,NAS,ISS IBA IEA,IBA TAS IEA,IDA IMP ISS TAS NAS IEA,IEA,IBA,ISS IBA TAS IEA,IMP IBA,ISS IEA,IMP IGI ISS IEA,IEA,IDA IMP IGI IBA,IEA,IEP ISS IBA,IEA,IMP,TAS,IDA IMP IGI IBA IEA,TAS IEA,IDA IMP TAS IC,IEA,TAS,IDA IEA,IMP IBA,ISS IEA,ISS IBA IEA,IMP IBA,HMP,IDA IPI IMP IGI ISS IBA IEA,IMP NAS IEA,ISS IBA IEA,IDA IBA IEA,IBA IEA,IEA,IDA IEA,IMP IBA TAS IEA,IMP ISS IBA IEA,HDA IEA,IEA | 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|
| query_1 | TRUE | 0.000000006547855 | 6576 | 941 | 444 | 0.472 | 0.068 | GO:0016043 | GO:BP | cellular component organization | 18092 | 5674 | GO:0071840 | IEA,IMP IBA,IDA ISS IBA IEA,IEA,IDA IMP IBA TAS IEA,IDA IBA IEA,IMP,TAS,ISS IEA,IDA IGI IEP NAS IEA,ISS IEA,IMP IBA TAS,IDA,ISS IEA,IEA,ISS IBA IEA,IEA,ISS IEA,IDA IMP ISS IEA,IDA IBA IEA,IEA,IMP TAS,IMP ISS IBA IEA,NAS,IMP IBA,IDA IBA,ISS TAS IEA,IDA IMP NAS,TAS,IMP,IDA,IBA,IDA IMP IBA,IEA,IBA IEA,TAS,IDA IMP IBA IEA,IDA IBA TAS IEA,IMP,IMP,TAS,IDA IMP IBA IEA,IMP IEA,ISS IEA,TAS,ISS TAS IEA,IDA ISS IBA IEA,TAS IEA,IMP IGI ISS TAS,IDA TAS,IDA IMP IBA IEA,IDA IEA,IEA,IDA,ISS IEA,IMP,IMP IEA,IDA IMP IEA,IMP IBA,ISS IBA IEA,IMP ISS IBA IEA,IEA,IBA,IMP IGI IEP IBA TAS IEA,IMP ISS IBA TAS IEA,IBA,IBA TAS IEA,ISS IEA,IEA,IBA IEA,IEA,IMP,IMP IBA IC IEA,IMP,IEA,ISS IBA IEA,IDA IMP ISS IBA IEA,IEP,IEA,IEA,ISS,IBA,IBA,IBA,IDA IEA,ISS TAS IEA,IEA,IBA,IMP,NAS,IDA TAS IEA,IBA TAS NAS,IDA IMP ISS IBA IEA,IDA,IDA ISS TAS IEA,IDA IMP IBA NAS IEA,ISS IBA IEA,IEA,IMP ISS IEA,TAS,IGI TAS,IEA,ISS TAS IEA,TAS,NAS,IMP ISS IBA TAS IEA,TAS,IMP,IEA,IMP IBA IEA,ISS IEA,TAS,IMP,IMP IBA TAS,IGI TAS,IEA,IMP,IMP ISS IBA IEA,IMP,IDA IBA NAS IEA,IMP ISS TAS IEA,IDA,IBA TAS,IEA,IEA,IPI IMP IBA IEA,IBA,IDA IBA,IDA IMP IBA IEA,IMP IBA IEA,IDA,TAS,TAS,IBA,IMP,IBA,IEA,IDA IMP IGI TAS IEA,IDA IMP IGI IBA TAS IEA,IMP,IMP,IDA IGI ISS,ISS IBA,IEA,TAS,IMP IGI IBA,IDA IEA,IMP IEA,ISS IEA,IDA IEA,IMP IBA,ISS IBA IEA,IDA TAS,IMP IBA TAS IEA,IDA IMP IBA TAS IEA,TAS IEA,IEA,IDA,IMP,IEA,IDA TAS,IBA IEA,TAS,IEA,IDA IBA,IEA,IEA,ISS IBA IEA,ISS IBA IEA,IDA IBA IEA,IMP,IMP,ISS IBA IEA,IMP IBA,ISS IEA,IEA,TAS,IMP TAS,IBA TAS,IMP,IMP,ISS IEA,IEA,IDA,IEA,TAS,TAS,ISS IBA,IDA IGI TAS IEA,IDA IMP ISS,TAS,IEA,ISS IBA TAS IEA,IEA,TAS,TAS,IEA,IBA IEA,TAS,IMP IBA IEA,IBA TAS,IBA IEA,IMP ISS IEA,TAS,TAS,IDA ISS IEA,IMP IEA,IBA,IBA IEA,IBA,TAS,IMP IEA,TAS,IMP IBA IEA,ISS IEA,IMP IBA TAS IEA,IMP IBA,TAS NAS,IMP,IMP IBA IEA,ISS TAS IEA,IMP IBA,IMP,TAS IEA,IDA IBA,IBA IEA,IBA TAS NAS IEA,TAS,IDA IBA IEA,IMP IGI ISS IEA,TAS NAS IEA,IMP IBA,IDA IMP ISS IBA,ISS IEA,IMP,IDA IBA TAS IEA,ISS IBA TAS IEA,IMP IBA,IEA,TAS,IMP IBA,IDA ISS IBA NAS IEA,IMP NAS IEA,IMP IGI ISS IBA,IDA IEA,ISS TAS IEA,TAS,IDA TAS IEA,IMP IBA,IDA IBA IEA,IBA TAS,IEA,IBA,IBA TAS IEA,TAS IEA,TAS IEA,IBA NAS IEA,IDA ISS IBA NAS,IMP IGI NAS IEA,IEA,IBA IEA,IMP IEA,IDA IBA IEA,TAS,IEA,IBA,IDA IBA TAS,IMP,IDA IMP ISS IBA TAS IEA,IDA IEA,TAS,IDA IEA,IMP,IDA IEA,IMP IBA IEA,IEA,IEA,IBA TAS,IBA IEA,TAS,IMP,IEA,IMP IBA TAS IEA,IEA,IEA,IEA,IBA NAS IEA,TAS,IEA,ISS IEA,IDA IMP HMP ISS IEA,IDA IEA,IEA,TAS,TAS,NAS,IDA,IMP,IMP IBA,ISS IBA IEA,IBA,IBA NAS IEA,IBA TAS,IMP,IMP,ISS IEA,ISS TAS,IDA IMP IEA,IMP,IMP IBA IEA,IEA,IEA,IMP IEA,NAS,IBA NAS IEA,TAS,IEA,IBA IEA,IEA,IBA,IDA IMP ISS IBA,TAS,IBA IEA,IDA,TAS,TAS,IBA IEA,IMP IBA IEA,IMP IBA,TAS,IBA IEA,IDA ISS IEA,TAS,ISS TAS,IMP IBA,IMP,TAS,IMP IBA IEA,IMP,IEA,TAS IEA,TAS,ISS IBA TAS IEA,IDA IBA IEA,TAS IEA,IDA ISS,IDA,IDA IBA TAS,IEA,IBA,IBA IC IEA,TAS,IEA,IMP IEA,IDA IBA,ISS IBA IEA,IMP TAS,IMP,IDA IMP,TAS,TAS,TAS,IDA,IEA,IDA IMP IBA IEA,IDA IMP IBA IEA,ISS,IMP IEA,IMP,IMP,IMP IBA IEA,ISS,ISS IBA IEA,ISS IEA,IBA IEA,IMP IEA,ISS IBA,IBA TAS IEA,IMP ISS,IBA,IMP,IEA,IBA,ISS TAS IEA,IBA,IMP,IDA,IDA IMP IBA TAS IEA,IBA,IMP IEA,IDA TAS IEA,IMP,IDA IMP IGI ISS IBA TAS IEA,TAS,IDA,IDA IMP IEA,IEA,ISS IEA,IMP IBA,IDA IEA,IBA IEA,IDA IMP IBA,IBA NAS IEA,IMP,IDA IMP IGI TAS,NAS,ISS IBA IEA,IBA TAS IEA,IDA IMP ISS TAS NAS IEA,IEA,IBA,ISS IBA TAS IEA,IMP IBA,ISS IEA,IMP IGI ISS IEA,IEA,IDA IMP IGI IBA,IEA,IEP ISS IBA,IEA,IMP,TAS,IDA IMP IGI IBA IEA,TAS IEA,IDA IMP TAS IC,IEA,TAS,IDA IEA,IMP IBA,ISS IEA,ISS IBA IEA,IMP IBA,HMP,IDA IPI IMP IGI ISS IBA IEA,IMP NAS IEA,ISS IBA IEA,IDA IBA IEA,IBA IEA,IEA,IDA IEA,IEA,IMP ISS IBA IEA,HDA IEA,IEA | ENSG00000001084,ENSG00000001460,ENSG00000001617,ENSG00000002016,ENSG00000002330,ENSG00000002822,ENSG00000002919,ENSG00000003056,ENSG00000003137,ENSG00000003393,ENSG00000003402,ENSG00000003509,ENSG00000003756,ENSG00000004139,ENSG00000004142,ENSG00000004399,ENSG00000004468,ENSG00000004478,ENSG00000004487,ENSG00000004700,ENSG00000004777,ENSG00000004779,ENSG00000004838,ENSG00000004866,ENSG00000004897,ENSG00000004961,ENSG00000004975,ENSG00000005007,ENSG00000005020,ENSG00000005022,ENSG00000005100,ENSG00000005108,ENSG00000005156,ENSG00000005175,ENSG00000005194,ENSG00000005249,ENSG00000005302,ENSG00000005339,ENSG00000005436,ENSG00000005448,ENSG00000005469,ENSG00000005471,ENSG00000005483,ENSG00000005810,ENSG00000005844,ENSG00000005884,ENSG00000005893,ENSG00000006125,ENSG00000006210,ENSG00000006451,ENSG00000006453,ENSG00000006459,ENSG00000006468,ENSG00000006530,ENSG00000006607,ENSG00000006625,ENSG00000006695,ENSG00000006712,ENSG00000006715,ENSG00000006740,ENSG00000006747,ENSG00000006831,ENSG00000006837,ENSG00000007047,ENSG00000007168,ENSG00000007237,ENSG00000007255,ENSG00000007341,ENSG00000007372,ENSG00000007392,ENSG00000007402,ENSG00000007516,ENSG00000007923,ENSG00000007944,ENSG00000008056,ENSG00000008083,ENSG00000008086,ENSG00000008128,ENSG00000008294,ENSG00000008300,ENSG00000008311,ENSG00000008324,ENSG00000008382,ENSG00000008516,ENSG00000008710,ENSG00000008735,ENSG00000008838,ENSG00000008853,ENSG00000009307,ENSG00000009844,ENSG00000009954,ENSG00000010017,ENSG00000010244,ENSG00000010270,ENSG00000010278,ENSG00000010292,ENSG00000010319,ENSG00000010322,ENSG00000010361,ENSG00000010610,ENSG00000010704,ENSG00000010803,ENSG00000010810,ENSG00000011009,ENSG00000011021,ENSG00000011143,ENSG00000011201,ENSG00000011243,ENSG00000011258,ENSG00000011295,ENSG00000011347,ENSG00000011405,ENSG00000011422,ENSG00000011426,ENSG00000011465,ENSG00000011485,ENSG00000011523,ENSG00000011600,ENSG00000011638,ENSG00000012048,ENSG00000012061,ENSG00000012124,ENSG00000012171,ENSG00000012211,ENSG00000012232,ENSG00000013016,ENSG00000013275,ENSG00000013297,ENSG00000013573,ENSG00000013810,ENSG00000014123,ENSG00000014138,ENSG00000014216,ENSG00000014257,ENSG00000014919,ENSG00000015133,ENSG00000015171,ENSG00000015285,ENSG00000015475,ENSG00000015676,ENSG00000017260,ENSG00000017427,ENSG00000018189,ENSG00000018408,ENSG00000018510,ENSG00000019144,ENSG00000019485,ENSG00000019549,ENSG00000019582,ENSG00000019991,ENSG00000019995,ENSG00000020129,ENSG00000020426,ENSG00000020922,ENSG00000021574,ENSG00000021645,ENSG00000021762,ENSG00000022267,ENSG00000023041,ENSG00000023171,ENSG00000023228,ENSG00000023287,ENSG00000023330,ENSG00000023516,ENSG00000023734,ENSG00000023902,ENSG00000023909,ENSG00000024048,ENSG00000024422,ENSG00000025293,ENSG00000025434,ENSG00000025708,ENSG00000025770,ENSG00000025772,ENSG00000026025,ENSG00000026036,ENSG00000026103,ENSG00000026508,ENSG00000027001,ENSG00000027075,ENSG00000027847,ENSG00000028137,ENSG00000028310,ENSG00000028528,ENSG00000028839,ENSG00000029639,ENSG00000029725,ENSG00000029993,ENSG00000030110,ENSG00000030582,ENSG00000031691,ENSG00000032219,ENSG00000032742,ENSG00000033178,ENSG00000033327,ENSG00000033627,ENSG00000033800,ENSG00000034510,ENSG00000034677,ENSG00000034693,ENSG00000034713,ENSG00000035115,ENSG00000035403,ENSG00000035862,ENSG00000035928,ENSG00000036054,ENSG00000036257,ENSG00000036549,ENSG00000037042,ENSG00000038210,ENSG00000038295,ENSG00000038382,ENSG00000038427,ENSG00000038532,ENSG00000038945,ENSG00000039068,ENSG00000039139,ENSG00000039319,ENSG00000039650,ENSG00000040275,ENSG00000040608,ENSG00000040633,ENSG00000041880,ENSG00000041982,ENSG00000042286,ENSG00000042317,ENSG00000042493,ENSG00000042753,ENSG00000043143,ENSG00000044090,ENSG00000044115,ENSG00000044459,ENSG00000044524,ENSG00000044574,ENSG00000046604,ENSG00000046647,ENSG00000046651,ENSG00000046653,ENSG00000046889,ENSG00000047249,ENSG00000047410,ENSG00000047579,ENSG00000047648,ENSG00000047849,ENSG00000048052,ENSG00000048342,ENSG00000048544,ENSG00000048649,ENSG00000048707,ENSG00000048740,ENSG00000049089,ENSG00000049167,ENSG00000049192,ENSG00000049245,ENSG00000049540,ENSG00000049541,ENSG00000049618,ENSG00000049759,ENSG00000049768,ENSG00000049860,ENSG00000049883,ENSG00000050327,ENSG00000050405,ENSG00000050555,ENSG00000050748,ENSG00000050767,ENSG00000050820,ENSG00000051009,ENSG00000051180,ENSG00000051341,ENSG00000051382,ENSG00000051523,ENSG00000051620,ENSG00000052795,ENSG00000052841,ENSG00000053372,ENSG00000053501,ENSG00000053747,ENSG00000053900,ENSG00000054116,ENSG00000054148,ENSG00000054267,ENSG00000054282,ENSG00000054523,ENSG00000054598,ENSG00000054654,ENSG00000054793,ENSG00000055130,ENSG00000055163,ENSG00000055332,ENSG00000055483,ENSG00000055609,ENSG00000055917,ENSG00000055950,ENSG00000056558,ENSG00000056736,ENSG00000057019,ENSG00000057252,ENSG00000057294,ENSG00000057663,ENSG00000057935,ENSG00000058063,ENSG00000058085,ENSG00000058262,ENSG00000058272,ENSG00000058335,ENSG00000058404,ENSG00000058453,ENSG00000058729,ENSG00000058804,ENSG00000058866,ENSG00000059915,ENSG0000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|
| query_1 | TRUE | 0.000001767254615 | 3562 | 941 | 260 | 0.276 | 0.073 | GO:0051641 | GO:BP | cellular localization | 18092 | 16066 | GO:0009987, GO:0051179 | IEA,ISS TAS IEA,TAS,TAS,TAS IEA,IDA IBA,IEA,IBA TAS IEA,IEA,IBA,IMP,IDA IMP IBA IEA,IEA,IEA,TAS,IBA TAS NAS,TAS,TAS,TAS,IDA,IMP TAS,IDA,IMP ISS IBA TAS IEA,IEA,IEA,IGI,IDA IEA,IDA,TAS,IMP,IMP IBA IEA,IBA IEA,IMP,IMP TAS,IDA IMP IGI ISS IBA TAS IEA,IBA TAS,IEA,IDA IMP,TAS,IBA TAS NAS IEA,IEA,IEA,IEA,IDA IMP,TAS,TAS,ISS IEA,IBA,IMP IBA TAS,TAS,IBA TAS,IDA,TAS,IDA IEA,IEA,IMP IEA,ISS TAS IEA,TAS,IDA,ISS IEA,TAS,IBA,IMP,IMP TAS,TAS,IDA IMP IGI IBA IEA,TAS,TAS,TAS,TAS,IBA IEA,IEA,IDA TAS IEA,IMP,TAS,ISS,TAS,ISS IEA,TAS,ISS IEA,TAS,TAS,IMP ISS IEA,IEA,IBA,TAS,IEA,TAS,IGI ISS IBA IEA,ISS,IMP IBA,IMP IBA TAS IEA,IBA TAS IEA,TAS,TAS,IBA TAS,TAS,TAS,IMP IBA NAS IEA,ISS IEA,IDA TAS IEA,IEA,TAS,IMP IBA,IBA IEA,IDA ISS,IBA TAS,ISS,TAS,IEA,IBA,IMP IBA,IDA,IMP TAS,TAS,IDA IMP IEA,IDA IMP,ISS IEA,IDA,TAS,IBA,IDA IMP,IEA,IMP IBA,IMP,IMP IBA IEA,ISS IBA TAS IEA,IDA IBA,IMP,ISS IBA IEA,IEA,ISS IEA,IMP IBA,IDA,IMP,TAS,TAS,ISS IBA,IDA IMP ISS IBA TAS IEA,ISS IBA IEA,ISS IBA IEA,IMP IGI,IMP IBA NAS IEA,IDA IBA,TAS IEA,IBA,IDA TAS IEA,IDA,TAS,ISS IEA,IMP,IMP IEA,TAS,TAS IEA,IDA IBA TAS IEA,TAS,IMP IBA,IMP IBA TAS,IBA TAS IEA,IEA,TAS,ISS IBA IEA,IBA,IMP ISS IEA,IMP,HMP,IEA,TAS,IMP IBA,TAS,IEA,TAS,IMP ISS IBA,IEA,IMP IEA,IDA IC,IMP IBA TAS,IMP,IMP TAS,TAS,IDA,TAS,ISS,IMP,IMP IBA IEA,IDA TAS IEA,ISS IEA,TAS,TAS,IBA,TAS,IMP IBA,IBA,IEA,IDA ISS IEA,IDA IBA,TAS,TAS,ISS,IDA,TAS,IMP ISS IBA TAS IEA,IBA,IDA ISS IBA TAS IEA,IDA IBA IEA,IEA,IBA,IBA,IBA,TAS,IMP,IMP,IEA,IMP IEA,IDA,IEA,IMP,IBA TAS IEA,IMP,IMP IBA,TAS,TAS,IEA,ISS IBA TAS IEA,IMP IGI TAS,ISS IEA,ISS IEA,IBA,IBA IEA,IDA,TAS,IMP,IDA IBA,TAS IEA,IMP,IDA IBA TAS,IDA IMP IBA NAS IEA,NAS,ISS TAS,IDA,IDA IPI IBA,IMP IBA TAS NAS IEA,IMP,IPI IBA,IEA,TAS,TAS,IEA,IMP IEA,IMP,IDA IBA,ISS IEA,HMP,ISS IEA,IEA,TAS,TAS IEA,IMP,IMP,ISS IEA | ENSG00000000457,ENSG00000000938,ENSG00000001036,ENSG00000001561,ENSG00000002330,ENSG00000002822,ENSG00000002919,ENSG00000003056,ENSG00000003393,ENSG00000004059,ENSG00000004487,ENSG00000004766,ENSG00000004838,ENSG00000004975,ENSG00000005007,ENSG00000005243,ENSG00000005249,ENSG00000005379,ENSG00000005469,ENSG00000005700,ENSG00000005844,ENSG00000005884,ENSG00000005893,ENSG00000006042,ENSG00000006125,ENSG00000006210,ENSG00000006451,ENSG00000006530,ENSG00000006534,ENSG00000006712,ENSG00000006715,ENSG00000006740,ENSG00000006747,ENSG00000007047,ENSG00000007168,ENSG00000007255,ENSG00000007372,ENSG00000007516,ENSG00000008018,ENSG00000008056,ENSG00000008086,ENSG00000008130,ENSG00000008277,ENSG00000008294,ENSG00000008394,ENSG00000008516,ENSG00000008710,ENSG00000008869,ENSG00000008952,ENSG00000008988,ENSG00000009844,ENSG00000010270,ENSG00000010278,ENSG00000010610,ENSG00000010671,ENSG00000010704,ENSG00000010810,ENSG00000011143,ENSG00000011243,ENSG00000011347,ENSG00000011422,ENSG00000011454,ENSG00000011523,ENSG00000011600,ENSG00000012779,ENSG00000013016,ENSG00000013364,ENSG00000013563,ENSG00000014216,ENSG00000014257,ENSG00000015133,ENSG00000015285,ENSG00000015475,ENSG00000015676,ENSG00000017427,ENSG00000018189,ENSG00000018280,ENSG00000018408,ENSG00000018510,ENSG00000019582,ENSG00000019991,ENSG00000021355,ENSG00000021574,ENSG00000021645,ENSG00000023041,ENSG00000023318,ENSG00000023516,ENSG00000023697,ENSG00000024422,ENSG00000025039,ENSG00000025772,ENSG00000025796,ENSG00000025800,ENSG00000026297,ENSG00000026508,ENSG00000027001,ENSG00000027075,ENSG00000028137,ENSG00000028528,ENSG00000029725,ENSG00000030066,ENSG00000030110,ENSG00000030582,ENSG00000031691,ENSG00000031823,ENSG00000032389,ENSG00000032742,ENSG00000033327,ENSG00000033627,ENSG00000034053,ENSG00000034510,ENSG00000034693,ENSG00000034713,ENSG00000035403,ENSG00000035862,ENSG00000036054,ENSG00000036257,ENSG00000036530,ENSG00000037474,ENSG00000038002,ENSG00000038532,ENSG00000039068,ENSG00000039139,ENSG00000039319,ENSG00000039523,ENSG00000040275,ENSG00000041353,ENSG00000041802,ENSG00000041880,ENSG00000042317,ENSG00000042753,ENSG00000044115,ENSG00000044459,ENSG00000044524,ENSG00000044574,ENSG00000046647,ENSG00000046651,ENSG00000046653,ENSG00000047410,ENSG00000047579,ENSG00000047621,ENSG00000047849,ENSG00000047932,ENSG00000048140,ENSG00000048342,ENSG00000048707,ENSG00000049245,ENSG00000049759,ENSG00000049860,ENSG00000050438,ENSG00000051009,ENSG00000051108,ENSG00000051128,ENSG00000051523,ENSG00000051596,ENSG00000051620,ENSG00000053770,ENSG00000053918,ENSG00000054116,ENSG00000054148,ENSG00000054282,ENSG00000054523,ENSG00000054611,ENSG00000054654,ENSG00000055118,ENSG00000055483,ENSG00000055732,ENSG00000055955,ENSG00000057294,ENSG00000057608,ENSG00000057663,ENSG00000058063,ENSG00000058262,ENSG00000058272,ENSG00000058453,ENSG00000058668,ENSG00000058673,ENSG00000058729,ENSG00000058804,ENSG00000059804,ENSG00000060656,ENSG00000060971,ENSG00000061987,ENSG00000062038,ENSG00000062650,ENSG00000062725,ENSG00000063176,ENSG00000063177,ENSG00000063244,ENSG00000063660,ENSG00000064012,ENSG00000064102,ENSG00000064201,ENSG00000064270,ENSG00000064300,ENSG00000064419,ENSG00000064601,ENSG00000064666,ENSG00000064687,ENSG00000064692,ENSG00000064703,ENSG00000065000,ENSG00000065054,ENSG00000065150,ENSG00000065308,ENSG00000065320,ENSG00000065491,ENSG00000065665,ENSG00000065882,ENSG00000065883,ENSG00000065978,ENSG00000066027,ENSG00000066044,ENSG00000066279,ENSG00000066294,ENSG00000066923,ENSG00000067066,ENSG00000067167,ENSG00000067182,ENSG00000067208,ENSG00000067225,ENSG00000067560,ENSG00000067606,ENSG00000067715,ENSG00000067900,ENSG00000068001,ENSG00000068305,ENSG00000068354,ENSG00000068400,ENSG00000068615,ENSG00000068650,ENSG00000068654,ENSG00000068724,ENSG00000068885,ENSG00000068912,ENSG00000069248,ENSG00000069329,ENSG00000069399,ENSG00000069424,ENSG00000069849,ENSG00000069869,ENSG00000069974,ENSG00000070010,ENSG00000070018,ENSG00000070087,ENSG00000070182,ENSG00000070366,ENSG00000070367,ENSG00000070371,ENSG00000070423,ENSG00000070540,ENSG00000070718,ENSG00000070770,ENSG00000070831,ENSG00000071054,ENSG00000071082,ENSG00000071127,ENSG00000071189,ENSG00000071537,ENSG00000071553 |
| query_1 | TRUE | 0.000001767254615 | 10855 | 941 | 652 | 0.693 | 0.060 | GO:0044237 | GO:BP | cellular metabolic process | 18092 | 12740 | GO:0008152, GO:0009987 | IDA IBA TAS IEA,IEA,IDA IMP ISS IBA TAS IEA,TAS,IDA IMP IBA TAS IEA,IDA ISS IBA TAS IEA,IBA TAS IEA,IDA,IBA IEA,IDA IMP IBA TAS IEA,IDA ISS IBA TAS IEA,IDA TAS IEA,IDA IEA,IBA,IDA IEA,IBA,ISS IBA IEA,IEA,IMP IEA,IDA IBA TAS IEA,IBA TAS IEA,IEA,IDA IEA,IDA IBA IEA,TAS,IBA TAS IEA,IMP,IBA IEA,IDA IMP ISS IBA IEA,IBA TAS,IBA IEA,IDA IBA TAS IEA,IMP TAS NAS IEA,IMP ISS TAS IEA,IDA IBA IEA,IDA IBA TAS IEA,IDA IBA,IDA IMP IEA,IDA IMP IBA TAS NAS IEA,IDA TAS IEA,IDA ISS IBA IEA,IDA IMP IBA TAS IEA,IBA IEA,IEA,IBA IEA,IDA TAS IEA,IDA IMP IBA IEA,IDA ISS IBA TAS IEA,TAS,IMP IBA TAS NAS IEA,IMP,IDA IMP ISS TAS IEA,IMP ISS IEA,IBA,IDA IEA,IBA IEA,IDA IMP IEA,IDA ISS IBA TAS NAS IEA,ISS TAS IEA,IBA IEA,IMP ISS IBA IEA,ISS TAS IEA,IDA IBA,IMP TAS NAS,IEA,TAS,IEA,TAS,TAS IEA,IDA IBA TAS IEA,IGI ISS,IDA ISS IBA IEA,IDA IEA,IDA IBA TAS 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|
| query_1 | TRUE | 0.000024193272382 | 6466 | 941 | 417 | 0.443 | 0.064 | GO:0048518 | GO:BP | positive regulation of biological process | 18092 | 14903 | GO:0008150, GO:0050789 | HMP,IMP ISS TAS IEA,IDA TAS IEA,IEA,ISS IBA,IMP,IDA IEA,IBA,IBA,IDA IMP ISS IBA TAS IEA,IBA,IEA,IDA IC IEA,IMP IBA,IEP IBA IEA,IDA TAS,IDA IEA,IEA,IBA TAS,IMP IBA IEA,IDA IMP ISS IBA IEA,IBA,ISS IEA,IBA,IDA IMP ISS IEA,IDA IMP,IMP,TAS,IDA ISS IBA IEA,TAS,IDA IMP ISS IBA TAS,IDA IMP,IMP,IDA IEA,IDA IEA,IDA IBA,IMP,ISS,IMP IBA IEA,IEA,IDA IMP IGI IEP ISS IBA TAS IEA,IBA,IDA IMP IBA IEA,ISS IBA IEA,IDA,IDA IMP IBA,IEA,IDA IEA,IBA IEA,IBA IEA,IMP,IMP ISS,ISS IEA,IBA,IDA IMP NAS,IMP,IMP,TAS,IDA IMP ISS IEA,IEA,IMP,IBA IEA,IEA,IDA IBA,TAS,ISS IEA,ISS IBA IEA,IEA,IEA,IMP IBA TAS IEA,IBA IEA,IBA,ISS IEA,IDA IBA,IDA,IDA,IEA,IDA IEA,IDA IBA TAS IEA,IEA,IMP ISS IEA,TAS,ISS IEA,IDA,IEA,IBA,IMP,IDA IBA TAS NAS IEA,TAS IEA,IDA IMP IGI ISS IEA,IDA ISS IBA TAS IEA,IDA IBA IEA,IDA IMP,IMP,IBA,IEA,IMP,IMP,IMP,IMP,IDA IGI IEA,HMP IEA,IEA,IMP ISS IBA IEA,IDA IMP IBA TAS IEA,ISS TAS IEA,IDA IMP IBA TAS,IBA,IGI IBA,IEA,IMP,ISS IEA,IDA IMP ISS IBA IEA,TAS IEA,IEA,IBA TAS IEA,IMP,IMP TAS,IDA IBA,IDA IMP,IEA,IDA IMP,IMP ISS IEA,IEA,TAS,IMP,IBA IEA,IDA IEA,IDA TAS IEA,IDA IMP IGI IBA TAS IEA,IDA,HMP,IDA IMP IGI,IDA ISS,ISS IEA,IDA IGI ISS IBA TAS IEA,IMP IGI,IDA IMP,IMP IEA,IDA IMP ISS IBA IEA,IDA IBA TAS NAS IEA,IMP IBA,IDA IBA IEA,IBA,IEA,IDA,IDA ISS IEA,IDA IMP TAS,IMP IEA,IDA,IDA,IDA ISS IBA,IMP,IBA IEA,IDA IBA TAS,ISS IEA,IMP IBA NAS,IDA,IDA IMP IBA IEA,IMP IEA,IMP IEA,IDA IMP IBA TAS,IDA IMP IBA,IDA IBA,IMP ISS TAS,ISS,IMP ISS IBA IEA,ISS IBA IEA,IEA,IDA ISS IEA,IDA IMP IBA IEA,IBA,IDA IMP ISS TAS IEA,IEA,IDA IMP ISS,IMP IBA,IEA,IDA,IDA ISS,IDA ISS IEA,IDA IMP IBA TAS IEA,IBA,IMP IBA,IMP IBA,TAS IEA,IEA,IEA,IEA,IMP IGI TAS,ISS IEA,IMP,IMP IGI IBA IEA,TAS,IMP IEA,ISS IBA IEA,IDA,IMP,IMP,IMP,IMP IBA,IMP IBA,TAS,IDA IGI,IEA,IDA,IDA IBA,IDA,IMP IBA,IEA,IDA IEP TAS,IGI ISS,TAS IEA,IDA IMP IBA,IMP TAS IEA,IMP,IMP ISS IEA,TAS,IMP ISS,ISS IEA,ISS IBA IEA,IMP,IDA IMP,IDA IBA,IMP,IDA IBA TAS IEA,IMP IBA,ISS IEA,IDA,IBA NAS,IDA ISS IBA NAS IEA,IDA IMP ISS IBA TAS IEA,IEA,IDA IMP TAS IEA,IBA,ISS IEA,ISS,IMP IEA,IDA NAS,IDA IMP,IDA,IMP IGI TAS,IDA IEA,IMP,IDA,IBA,IBA,IDA IMP,IDA IMP IBA,IMP IEA,IEA,IMP IEA,IEA,IDA IMP ISS NAS IEA,ISS IEA,IDA IBA,IDA,TAS,IDA IBA TAS IEA,IDA IEP IBA TAS,IMP ISS IEA,HMP,IBA,IDA IMP,IBA,ISS IEA,IEA,IEP IBA,IMP,ISS,IEA,IGI IEA,IDA IMP IEA,IEA,IMP,IMP,IDA IMP IBA,ISS TAS,ISS,IMP,TAS,IDA,IDA IMP,IEA,IDA TAS,ISS IC IEA,IMP ISS IBA IEA,IDA IMP IEA,IDA,IMP,IDA IMP ISS TAS,IDA,IMP,IEA,IEA,IEA,TAS,IEA,IMP IBA,IDA ISS IBA IEA,IDA,IBA,ISS IEA,IMP,IDA ISS IBA IEA,IDA IMP IEP ISS IBA TAS IEA,IMP IBA,IMP,IEA,IDA IMP TAS IEA,TAS IEA,IDA IMP ISS IBA IEA,IEA,IDA IEA,IMP,ISS,IBA,IEA,ISS,IGI ISS IEA,IBA IEA,IEA,IEA,IDA IEA,IEA,IDA,IMP IEA,ISS IEA,IMP,ISS IEA,IMP IBA TAS IEA,IDA IGI IBA IEA,IMP,IDA,IBA IEA,IBA TAS,IDA IBA,IDA IMP IEA,IMP,IDA IMP IGI IEA,IBA,IMP IBA,IEA,TAS,IEA,IDA,IDA IGI ISS IEA,TAS,IMP,IDA IMP IGI ISS IBA TAS IEA,IMP IEA,IEA,IDA IMP,IDA TAS,IEA,IMP IEP ISS TAS IEA,IMP ISS IEA,IEA,IDA IMP IBA NAS IEA,IDA IMP IEP TAS NAS IEA,IMP ISS IEA,IDA ISS IEA,IMP,IEA,IMP IGI ISS IEA,ISS TAS IEA,IDA ISS IEA,IDA IMP ISS IEA,IDA,IMP IGI IBA TAS IEA,IDA IGI IBA TAS IEA,IMP ISS IEA,IDA ISS IEA,TAS,IMP,TAS IEA,IMP ISS IEA,IEA,IEA,IEA,IMP IGI IEA,IDA IMP IGI IEA,TAS,IDA IMP IEA,IEA,IDA IMP ISS IEA,ISS IEA,IDA,IDA IMP IBA,IEA,IMP IGI IBA,IDA IMP IBA,IMP IGI IBA IEA,IMP,IDA,IDA IMP,IDA IMP,IEA,IDA,IDA IMP ISS TAS IEA,IDA IBA,HMP,IDA,IDA IMP ISS TAS IEA,IMP,ISS IEA,IDA IMP IEA,IMP ISS IBA,IBA IEA,IDA IEA,IDA,IMP IEA,IMP,ISS IEA,IDA IMP ISS IBA TAS,ISS IBA IEA,IBA IEA,IEA | ENSG00000000003,ENSG00000000938,ENSG00000000971,ENSG00000001084,ENSG00000001167,ENSG00000001460,ENSG00000001561,ENSG00000001617,ENSG00000001629,ENSG00000002330,ENSG00000002586,ENSG00000003137,ENSG00000003393,ENSG00000003400,ENSG00000003402,ENSG00000003756,ENSG00000004139,ENSG00000004142,ENSG00000004399,ENSG00000004468,ENSG00000004487,ENSG00000004660,ENSG00000004838,ENSG00000004897,ENSG00000004975,ENSG00000005007,ENSG00000005022,ENSG00000005075,ENSG00000005100,ENSG00000005249,ENSG00000005339,ENSG00000005471,ENSG00000005483,ENSG00000005810,ENSG00000005884,ENSG00000006016,ENSG00000006025,ENSG00000006047,ENSG00000006062,ENSG00000006125,ENSG00000006210,ENSG00000006283,ENSG00000006327,ENSG00000006432,ENSG00000006451,ENSG00000006453,ENSG00000006459,ENSG00000006468,ENSG00000006634,ENSG00000006638,ENSG00000006712,ENSG00000006747,ENSG00000006831,ENSG00000006837,ENSG00000007047,ENSG00000007062,ENSG00000007168,ENSG00000007264,ENSG00000007372,ENSG00000007402,ENSG00000007516,ENSG00000007866,ENSG00000007944,ENSG00000007968,ENSG00000008018,ENSG00000008083,ENSG00000008086,ENSG00000008130,ENSG00000008256,ENSG00000008294,ENSG00000008324,ENSG00000008382,ENSG00000008405,ENSG00000008441,ENSG00000008517,ENSG00000008710,ENSG00000008735,ENSG00000008838,ENSG00000009724,ENSG00000009830,ENSG00000009950,ENSG00000009954,ENSG00000010017,ENSG00000010072,ENSG00000010310,ENSG00000010319,ENSG00000010361,ENSG00000010610,ENSG00000010671,ENSG00000010704,ENSG00000010810,ENSG00000011198,ENSG00000011243,ENSG00000011304,ENSG00000011332,ENSG00000011347,ENSG00000011405,ENSG00000011422,ENSG00000011426,ENSG00000011451,ENSG00000011465,ENSG00000011485,ENSG00000011566,ENSG00000011600,ENSG00000012048,ENSG00000012061,ENSG00000012124,ENSG00000012171,ENSG00000012174,ENSG00000012232,ENSG00000012660,ENSG00000012779,ENSG00000012822,ENSG00000012983,ENSG00000013016,ENSG00000013275,ENSG00000013374,ENSG00000013503,ENSG00000013561,ENSG00000013573,ENSG00000013588,ENSG00000013725,ENSG00000014123,ENSG00000014164,ENSG00000014216,ENSG00000014257,ENSG00000014824,ENSG00000015153,ENSG00000015285,ENSG00000015475,ENSG00000015479,ENSG00000017260,ENSG00000017427,ENSG00000018189,ENSG00000018280,ENSG00000018408,ENSG00000019144,ENSG00000019485,ENSG00000019549,ENSG00000019582,ENSG00000019991,ENSG00000019995,ENSG00000020181,ENSG00000020256,ENSG00000020426,ENSG00000020577,ENSG00000020633,ENSG00000020922,ENSG00000021574,ENSG00000022267,ENSG00000022556,ENSG00000022840,ENSG00000023041,ENSG00000023287,ENSG00000023445,ENSG00000024422,ENSG00000025039,ENSG00000025156,ENSG00000025434,ENSG00000025800,ENSG00000026025,ENSG00000026103,ENSG00000026508,ENSG00000026950,ENSG00000027075,ENSG00000027697,ENSG00000028137,ENSG00000028277,ENSG00000028528,ENSG00000029153,ENSG00000029363,ENSG00000029993,ENSG00000030110,ENSG00000030419,ENSG00000030582,ENSG00000031691,ENSG00000032219,ENSG00000032389,ENSG00000033327,ENSG00000033800,ENSG00000034152,ENSG00000034677,ENSG00000035499,ENSG00000035664,ENSG00000035681,ENSG00000035862,ENSG00000035928,ENSG00000036054,ENSG00000036257,ENSG00000036530,ENSG00000036672,ENSG00000037280,ENSG00000038382,ENSG00000038532,ENSG00000038945,ENSG00000039068,ENSG00000039523,ENSG00000039650,ENSG00000040608,ENSG00000040633,ENSG00000041353,ENSG00000041357,ENSG00000041880,ENSG00000041982,ENSG00000041988,ENSG00000042286,ENSG00000042429,ENSG00000043093,ENSG00000043143,ENSG00000043462,ENSG00000044090,ENSG00000044115,ENSG00000044524,ENSG00000044574,ENSG00000046653,ENSG00000047188,ENSG00000047315,ENSG00000047410,ENSG00000047579,ENSG00000047621,ENSG00000048052,ENSG00000048540,ENSG00000048649,ENSG00000048707,ENSG00000049130,ENSG00000049167,ENSG00000049245,ENSG00000049541,ENSG00000049618,ENSG00000049759,ENSG00000049768,ENSG00000049860,ENSG00000050327,ENSG00000050344,ENSG00000050438,ENSG00000050628,ENSG00000050748,ENSG00000050820,ENSG00000051108,ENSG00000051180,ENSG00000051382,ENSG00000051523,ENSG00000051620,ENSG00000052795,ENSG00000053438,ENSG00000053900,ENSG00000053918,ENSG00000054118,ENSG00000054148,ENSG00000054267,ENSG00000054277,ENSG00000054523,ENSG00000054598,ENSG00000054654,ENSG00000054965,ENSG00000055118,ENSG00000055130,ENSG00000055163,ENSG00000055208,ENSG00000055332,ENSG00000055483,ENSG00000055609,ENSG00000055917,ENSG00000056558,ENSG00000056586,ENSG00000056736,ENSG00000056972,ENSG00000057252,ENSG00000057294,ENSG00000057657,ENSG00000057663,ENSG00000057757,ENSG00000057935,ENSG00000058056,ENSG00000058085,ENSG00000058272,ENSG00000058335,ENSG00000058404,ENSG00000058453,ENSG00000058600,ENSG00000058668,ENSG00000058729,ENSG00000059377,ENSG00000060069,ENSG00000060138,ENSG00000060237,ENSG00000060339,ENSG00000060656,ENSG00000061273,ENSG00000061676,ENSG00000061938,ENSG00000062038,ENSG00000062194,ENSG00000062282,ENSG00000062370,ENSG00000062598,ENSG00000062650,ENSG00000063169,ENSG00000063176,ENSG00000063244,ENSG00000063438,ENSG00000063660,ENSG00000063761,ENSG00000063978,ENSG00000064012,ENSG00000064042,ENSG00000064115,ENSG00000064270,ENSG00000064300,ENSG00000064309,ENSG00000064393,ENSG00000064489,ENSG00000064490,ENSG00000064545,ENSG00000064651,ENSG00000064655,ENSG00000064666,ENSG00000064687,ENSG00000064703,ENSG00000064932,ENSG00000064961,ENSG00000064989,ENSG00000064995,ENSG00000065000,ENSG00000065029,ENSG00000065135,ENSG00000065150,ENSG00000065243,ENSG00000065320,ENSG00000065361,ENSG00000065427,ENSG00000065526,ENSG00000065534,ENSG00000065559,ENSG00000065883,ENSG00000065970,ENSG00000065978,ENSG00000066027,ENSG00000066044,ENSG00000066056,ENSG00000066117,ENSG00000066136,ENSG00000066248,ENSG00000066279,ENSG00000066294,ENSG00000066336,ENSG00000066379,ENSG00000066427,ENSG00000066468,ENSG00000066777,ENSG00000066827,ENSG00000067066,ENSG00000067082,ENSG00000067141,ENSG00000067182,ENSG00000067225,ENSG00000067248,ENSG00000067369,ENSG00000067560,ENSG00000067606,ENSG00000067715,ENSG00000067798,ENSG00000067836,ENSG00000067900,ENSG00000067955,ENSG00000068001,ENSG00000068024,ENSG00000068028,ENSG00000068078,ENSG00000068305,ENSG00000068323,ENSG00000068366,ENSG00000068654,ENSG00000068745,ENSG00000068878,ENSG00000068903,ENSG00000068971,ENSG00000069011,ENSG00000069122,ENSG00000069275,ENSG00000069329,ENSG00000069345,ENSG00000069399,ENSG00000069535,ENSG00000069667,ENSG00000069702,ENSG00000069849,ENSG00000069869,ENSG00000069956,ENSG00000069974,ENSG00000070018,ENSG00000070087,ENSG00000070371,ENSG00000070404,ENSG00000070476,ENSG00000070495,ENSG00000070614,ENSG00000070669,ENSG00000070756,ENSG00000070761,ENSG00000070770,ENSG00000070785,ENSG00000070831,ENSG00000070950,ENSG00000070961,ENSG00000071051,ENSG00000071054,ENSG00000071127,ENSG00000071242,ENSG00000071243,ENSG00000071282,ENSG00000071462,ENSG00000071553,ENSG00000071564,ENSG00000071575,ENSG00000071626,ENSG00000071794 |
| query_1 | TRUE | 0.000032046960665 | 2789 | 941 | 207 | 0.220 | 0.074 | GO:0008104 | GO:BP | protein localization | 18092 | 3549 | GO:0033036 | IEA,ISS IEA,ISS TAS IEA,IEA,IBA IEA,IEA,IEA,IBA IEA,IEA,IEA,IMP,IEA,IEA,IEA,IEA,TAS,TAS,IBA NAS IEA,TAS,IEA,IMP,IDA,IMP ISS IBA TAS IEA,IEA,IEA,IDA,IMP,IBA IEA,IBA IEA,IMP,IMP,IMP,IEA,IDA IMP IBA IEA,TAS,IMP,IEA,IEA,IEA,IEA,ISS IEA,IBA,IMP IBA TAS IEA,TAS,IEA,TAS IEA,IEA,IDA,IMP TAS,ISS TAS IEA,IEA,IDA,ISS IEA,IBA,IMP,IMP ISS IEA,ISS IEA,IGI IBA IEA,IEA,IMP,IDA TAS IEA,IMP,IMP,ISS,ISS IEA,TAS,ISS IEA,IBA,IBA IEA,ISS IBA IEA,ISS,ISS IEA,IMP IBA,IMP IBA TAS IEA,IBA TAS IEA,IBA TAS,TAS,IMP IEA,ISS IEA,IDA TAS IEA,IMP IBA,IBA IEA,ISS,IBA TAS,TAS,IEA,IBA,IMP IBA,IDA IEA,IMP,ISS IEA,IDA,IEA,IDA IMP,IMP IBA,IMP,IMP IBA IEA,ISS IEA,IBA IEA,IMP,ISS IBA IEA,IEA,ISS IEA,IMP IBA,IDA,IMP,ISS IEA,TAS,IDA IMP ISS IBA TAS IEA,IMP IBA NAS IEA,IDA IBA,IEA,IBA,IEA,IDA TAS,IDA,IMP,IEA,IEA,IMP IEA,TAS,IDA IBA TAS IEA,IBA,IEA,IEA,IEA,IEA,IBA,HMP,IMP IBA,IEA,IMP ISS IBA IEA,IMP,IDA,IMP IBA TAS,IMP,IMP TAS NAS IEA,IDA,TAS,IEA,IMP IBA IEA,TAS IEA,TAS,TAS,IBA,TAS,IMP,IMP,IBA,IEA,IDA ISS IEA,IDA IBA IEA,TAS,ISS,IEA,ISS,IDA,IMP IBA TAS IEA,IBA,IDA ISS IBA TAS IEA,IDA IBA IEA,IBA,ISS IEA,IBA IEA,IBA IEA,IMP,IMP,IEA,IMP,IEA,IEA,IDA IMP,IBA TAS IEA,IMP,IBA,IEA,IMP IGI,ISS IEA,IBA,ISS IEA,IBA IEA,IDA,IMP,IDA IBA,TAS IEA,IMP,IDA IBA TAS IEA,IDA IMP IBA IEA,NAS,ISS,IDA,IPI IBA,IEA,IMP,IPI,TAS,IEA,IEA,IBA,IEA,HMP,IEA,IEA,TAS,IMP IEA,IMP ISS IEA,TAS | ENSG00000000457,ENSG00000001630,ENSG00000002330,ENSG00000002919,ENSG00000003056,ENSG00000003147,ENSG00000003393,ENSG00000004059,ENSG00000004468,ENSG00000004478,ENSG00000004487,ENSG00000004766,ENSG00000004777,ENSG00000004838,ENSG00000004975,ENSG00000005007,ENSG00000005022,ENSG00000005243,ENSG00000005469,ENSG00000005810,ENSG00000005844,ENSG00000005884,ENSG00000005893,ENSG00000006042,ENSG00000006125,ENSG00000006530,ENSG00000006712,ENSG00000006715,ENSG00000006740,ENSG00000006747,ENSG00000007047,ENSG00000007168,ENSG00000007372,ENSG00000007384,ENSG00000007402,ENSG00000007516,ENSG00000008086,ENSG00000008130,ENSG00000008277,ENSG00000008300,ENSG00000008710,ENSG00000008869,ENSG00000008952,ENSG00000008988,ENSG00000009844,ENSG00000010310,ENSG00000010361,ENSG00000010610,ENSG00000010704,ENSG00000010810,ENSG00000011132,ENSG00000011243,ENSG00000011347,ENSG00000011454,ENSG00000011523,ENSG00000011600,ENSG00000012779,ENSG00000013016,ENSG00000013364,ENSG00000014123,ENSG00000015475,ENSG00000015676,ENSG00000017427,ENSG00000018189,ENSG00000018408,ENSG00000018510,ENSG00000019582,ENSG00000023041,ENSG00000023516,ENSG00000024422,ENSG00000025039,ENSG00000025434,ENSG00000025772,ENSG00000025796,ENSG00000025800,ENSG00000027001,ENSG00000027075,ENSG00000028528,ENSG00000029725,ENSG00000030066,ENSG00000031691,ENSG00000031823,ENSG00000032389,ENSG00000032742,ENSG00000033627,ENSG00000034053,ENSG00000034510,ENSG00000034693,ENSG00000034713,ENSG00000035403,ENSG00000036530,ENSG00000037474,ENSG00000038945,ENSG00000039068,ENSG00000039319,ENSG00000039523,ENSG00000040275,ENSG00000041353,ENSG00000041802,ENSG00000041880,ENSG00000042317,ENSG00000042753,ENSG00000044115,ENSG00000044459,ENSG00000044524,ENSG00000044574,ENSG00000046653,ENSG00000047249,ENSG00000047410,ENSG00000047932,ENSG00000048140,ENSG00000048342,ENSG00000048707,ENSG00000049245,ENSG00000049323,ENSG00000049759,ENSG00000050327,ENSG00000050748,ENSG00000051009,ENSG00000051108,ENSG00000051128,ENSG00000051596,ENSG00000053438,ENSG00000053501,ENSG00000053770,ENSG00000054148,ENSG00000054523,ENSG00000054611,ENSG00000055483,ENSG00000057294,ENSG00000057608,ENSG00000058262,ENSG00000058453,ENSG00000058668,ENSG00000058673,ENSG00000058729,ENSG00000058804,ENSG00000060656,ENSG00000060971,ENSG00000061987,ENSG00000062650,ENSG00000062725,ENSG00000063177,ENSG00000063244,ENSG00000063660,ENSG00000064012,ENSG00000064102,ENSG00000064115,ENSG00000064201,ENSG00000064270,ENSG00000064300,ENSG00000064419,ENSG00000064601,ENSG00000064651,ENSG00000064652,ENSG00000064687,ENSG00000064989,ENSG00000065000,ENSG00000065054,ENSG00000065150,ENSG00000065308,ENSG00000065491,ENSG00000065615,ENSG00000065665,ENSG00000065882,ENSG00000065978,ENSG00000066027,ENSG00000066044,ENSG00000066427,ENSG00000066777,ENSG00000066923,ENSG00000067066,ENSG00000067167,ENSG00000067182,ENSG00000067208,ENSG00000067606,ENSG00000067900,ENSG00000068001,ENSG00000068354,ENSG00000068366,ENSG00000068400,ENSG00000068615,ENSG00000068654,ENSG00000068724,ENSG00000068885,ENSG00000068912,ENSG00000069248,ENSG00000069329,ENSG00000069399,ENSG00000069424,ENSG00000069849,ENSG00000069869,ENSG00000069974,ENSG00000070010,ENSG00000070018,ENSG00000070366,ENSG00000070367,ENSG00000070371,ENSG00000070540,ENSG00000070718,ENSG00000070770,ENSG00000070831,ENSG00000071054,ENSG00000071082,ENSG00000071189,ENSG00000071537,ENSG00000071553 |
- Get a web link to share the results with your coworkers
### Web link ###
message("Getting a web link to view the results")
# Get a web link
gostres_link <- gost(query = gene_list,
organism = "hsapiens",
ordered_query = FALSE,
multi_query = FALSE,
significant = TRUE,
exclude_iea = FALSE,
measure_underrepresentation = FALSE,
evcodes = TRUE,
user_threshold = 0.05,
correction_method = "fdr",
domain_scope = "annotated",
custom_bg = NULL,
numeric_ns = "",
sources = NULL,
as_short_link = TRUE)
gostres_link[1] "https://biit.cs.ut.ee/gplink/l/FRcHo1TRSk"- Make a static plot
### Static plot ###
message("Generating a static plot")
# Static ggplot object
p <- gostplot(gostres, capped = FALSE, interactive = FALSE)
p
Static figure of the enrichment analysis.
- Highlight the
GO:0071840andHPA:0300000terms
### Highlight terms ###
message("Highlighting terms")
# Highlight terms
pp <- publish_gostplot(p,
highlight_terms = c("GO:0071840", "HPA:0300000"),
width = NA,
height = NA,
filename = NULL )
Static figure of the enrichment analysis with highlighted terms.
#pp- Produce a custom table with choosen results
# Table
publish_gosttable(gostres,
highlight_terms = gostres$result[c(1:2,10,50:52,64,69,71),],
use_colors = TRUE,
show_columns = c("source", "term_name", "term_size", "intersection_size"),
filename = NULL)
Custom table of the enrichment analysis with choosen results.
If you feel adventurous, you can try to do the same with multiple gene lists (for instance, clusters from the previous practical).
Save your session info
For the sake of traceability, store the specifications of your R environment in the report, with the command sessionInfo(). This will indicate the version of R as well as of all the libraries used in this notebook.
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /shared/ifbstor1/software/miniconda/envs/r-4.0.2/lib/libopenblasp-r0.3.10.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gprofiler2_0.2.0 knitr_1.30
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.20 purrr_0.3.4 colorspace_2.0-0 vctrs_0.3.6 generics_0.1.0 htmltools_0.5.1.1 viridisLite_0.3.0 yaml_2.2.1 utf8_1.2.1 plotly_4.9.3 rlang_0.4.10 pillar_1.5.1 later_1.1.0.1 glue_1.4.2 DBI_1.1.1
[17] lifecycle_1.0.0 stringr_1.4.0 munsell_0.5.0 gtable_0.3.0 htmlwidgets_1.5.3 evaluate_0.14 labeling_0.4.2 fastmap_1.1.0 httpuv_1.5.5 crosstalk_1.1.1 fansi_0.4.2 highr_0.8 Rcpp_1.0.6 xtable_1.8-4 scales_1.1.1 promises_1.2.0.1
[33] debugme_1.1.0 jsonlite_1.7.2 farver_2.1.0 mime_0.10 gridExtra_2.3 ggplot2_3.3.3 digest_0.6.27 stringi_1.5.3 dplyr_1.0.5 shiny_1.5.0 grid_4.0.2 tools_4.0.2 bitops_1.0-6 magrittr_2.0.1 lazyeval_0.2.2 RCurl_1.98-1.3
[49] tibble_3.1.0 crayon_1.4.1 tidyr_1.1.3 pkgconfig_2.0.3 ellipsis_0.3.1 data.table_1.14.0 assertthat_0.2.1 rmarkdown_2.5 httr_1.4.2 R6_2.5.0 compiler_4.0.2