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goseq-go-kegg-enrichment-analsis-tests.yml
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- doc: Test outline for goseq-go-kegg-enrichment-analsis
job:
Differential expression result:
class: File
location: https://zenodo.org/records/14033254/files/de-result.tabular
filetype: tabular
gene length:
class: File
location: https://zenodo.org/records/14033254/files/gene-length.tabular
filetype: tabular
KEGG pathways:
class: File
location: https://zenodo.org/records/14033254/files/kegg-pathways.tabular
filetype: tabular
Select genome to use: mm10
Select gene ID format: ensGene
outputs:
goseq Enrichment Table (Cellular Component):
asserts:
- that: "has_text_matching"
expression: "category\tover_represented_pvalue\tunder_represented_pvalue\tnumDEInCat\tnumInCat\tterm\tontology\tp_adjust_over_represented\tp_adjust_under_represented"
- that: "has_text_matching"
expression: "GO:0005737\t4.79[0-9]+e-08\t1\t4810\t8312\tcytoplasm\tCC\t9.31[0-9]+e-05\t1"
- that: "has_text_matching"
expression: "over_represented_pvalue"
- that: "has_text_matching"
expression: "under_represented_pvalue"
goseq Top Categories plot (Cellular Component):
asserts:
- that: "has_size"
size: 7078
goseq Differential Genes in each Category (Cellular Component):
asserts:
- that: "has_text_matching"
expression: "category\tde_genes"
- that: "has_text_matching"
expression: "GO:0005737\tENSMUSG00000045545,ENSMUSG00000029802,ENSMUSG00000058056"
goseq Differential Genes in each Category (Biological Process):
asserts:
- that: "has_text_matching"
expression: "category\tde_genes"
- that: "has_text_matching"
expression: "GO:0043254\tENSMUSG00000023951,ENSMUSG00000032060,ENSMUSG00000031284,"
goseq Top Categories plot (Biological Process):
asserts:
- that: "has_size"
size: 7092
goseq Enrichment Table (Biological Process):
asserts:
- that: "has_text_matching"
expression: "category\tover_represented_pvalue\tunder_represented_pvalue\tnumDEInCat\tnumInCat\tterm\tontology\tp_adjust_over_represented\tp_adjust_under_represented"
- that: "has_text_matching"
expression: "GO:0043254\t3.41[0-9]+e-07\t1\t239\t345\tregulation of protein-containing complex assembly\tBP\t0.0034[0-9]+\t1"
- that: "has_text_matching"
expression: "over_represented_pvalue"
- that: "has_text_matching"
expression: "under_represented_pvalue"
goseq Differential Genes in each Category (KEGG):
asserts:
- that: "has_text_matching"
expression: "category\tde_genes"
- that: "has_text_matching"
expression: "04540\tENSMUSG00000063358,ENSMUSG00000045136,ENSMUSG00000025856,ENSMUSG00000028019"
goseq Top Categories plot (Molecular Function):
asserts:
- that: "has_size"
size: 7166
goseq Enrichment Table (Molecular Function):
asserts:
- that: "has_text_matching"
expression: "category\tover_represented_pvalue\tunder_represented_pvalue\tnumDEInCat\tnumInCat\tterm\tontology\tp_adjust_over_represented\tp_adjust_under_represented"
- that: "has_text_matching"
expression: "GO:0005515\t1.4094[0-9]+e-07\t1\t3758\t6415\tprotein binding\tMF\t0.0006[0-9]+\t1"
- that: "has_text_matching"
expression: "over_represented_pvalue"
- that: "has_text_matching"
expression: "under_represented_pvalue"
goseq Differential Genes in each Category (Molecular Function):
asserts:
- that: "has_text_matching"
expression: "category\tde_genes"
- that: "has_text_matching"
expression: "GO:0005515\tENSMUSG00000045545,ENSMUSG00000029802,ENSMUSG00000058056,ENSMUSG00000004044,"
goseq Enrichment Table (KEGG):
asserts:
- that: "has_text_matching"
expression: "category\tover_represented_pvalue\tunder_represented_pvalue\tnumDEInCat\tnumInCat\tp_adjust_over_represented\tp_adjust_under_represented\tID\tName"
- that: "has_text_matching"
expression: "04540\t0.0031[0-9]+\t0.99[0-9]+\t47\t61\t0.46[0-9]+\t1\t04540\tGap junction - mmus"