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CLI Quickstart

Source notebook: ../../notebooks/01_cli_quickstart.ipynb

Start with the common bioinformatics case: a one-column list of human genes from an over-expression result, and return a table of enriched GO terms. This example uses 50 interferon/inflammatory genes and a prepared official GOA human/GO snapshot.

Output:

50input genes

Output:

Input gene list
gene_id
IFIT1
IFIT2
IFIT3
ISG15
MX1
OAS1
STAT1
IRF7
CXCL10
RSAD2
IFIH1
IFI6
IFI27
IFI35
IFI44 
mkdir -p notebooks/generated
genesets-rs run examples/human-go-enrich.yaml > notebooks/generated/quickstart_go.tsv
echo "Wrote notebooks/generated/quickstart_go.tsv"

Output:

Wrote notebooks/generated/quickstart_go.tsv

Output:

217enriched GO terms
50query genes
1.5e-48best adjusted p

Output:

Top enriched GO terms
target_id target_name overlap query_size target_size p_adjust_bonferroni
GO:0009615 response to virus 32 50 368 1.499e-48
GO:0051607 defense response to virus 29 50 226 3.048e-48
GO:0051707 response to other organism 39 50 1237 1.338e-44
GO:0043207 response to external biotic stimulus 39 50 1240 1.471e-44
GO:0009607 response to biotic stimulus 39 50 1278 4.809e-44
GO:0044419 biological process involved in interspecies interaction between organisms 39 50 1389 1.257e-42
GO:0006952 defense response 38 50 1289 6.566e-42
GO:0009605 response to external stimulus 39 50 1693 2.858e-39
GO:0140546 defense response to symbiont 32 50 736 1.101e-38
GO:0098542 defense response to other organism 32 50 744 1.562e-38
GO:0045087 innate immune response 30 50 626 6.192e-37
GO:0006955 immune response 36 50 1528 2.063e-35
GO:0002376 immune system process 38 50 2113 9.019e-34
GO:0034097 response to cytokine 29 50 844 3.471e-31
GO:1901652 response to peptide 29 50 857 5.410e-31

Broad GO terms are often expected at the very top. A useful first pass is to also inspect terms below a target-size threshold.

Output:

More specific enriched GO terms
target_id target_name overlap query_size target_size p_adjust_bonferroni
GO:0009615 response to virus 32 50 368 1.499e-48
GO:0051607 defense response to virus 29 50 226 3.048e-48
GO:0045071 negative regulation of viral genome replication 15 50 49 1.391e-28
GO:0048525 negative regulation of viral process 16 50 75 6.673e-28
GO:0045069 regulation of viral genome replication 16 50 78 1.339e-27
GO:0050792 regulation of viral process 17 50 140 2.027e-25
GO:1903900 regulation of viral life cycle 16 50 112 7.204e-25
GO:0140374 antiviral innate immune response 12 50 76 3.070e-18
GO:0034341 response to type II interferon 12 50 101 1.153e-16
GO:0034340 response to type I interferon 12 50 114 5.280e-16
GO:0140888 interferon-mediated signaling pathway 11 50 88 3.110e-15
GO:0031349 positive regulation of defense response 16 50 485 1.937e-14
GO:0071346 cellular response to type II interferon 9 50 60 1.349e-12
GO:0035456 response to interferon-beta 8 50 35 2.030e-12
GO:0071357 cellular response to type I interferon 10 50 106 2.946e-12
GO:0060337 type I interferon-mediated signaling pathway 9 50 67 3.876e-12
GO:0045089 positive regulation of innate immune response 13 50 327 4.789e-12
GO:0002833 positive regulation of response to biotic stimulus 13 50 357 1.490e-11
GO:0032728 positive regulation of interferon-beta production 7 50 42 2.083e-09
GO:0032481 positive regulation of type I interferon production 8 50 80 2.394e-09