Expression20 vs GO
Source notebook: ../../notebooks/02_expression20_eval.ipynb
This notebook runs 20 expression-derived MyGeneset/MSigDB signatures against an official GOA human/GO snapshot. The CLI does the enrichment; Python only summarizes the Parquet results.
python3 scripts/fetch_mygeneset_eval.py \
--manifest evals/expression20/sets.tsv \
--out-dir evals/expression20/generated \
--skip-existing
Output:
Using existing MyGeneset snapshot at evals/expression20/generated
python3 scripts/run_expression20_go_demo.py --skip-existing
Output:
reused_existing: notebooks/generated/expression20_go_now.parquet
metadata: notebooks/generated/expression20_go_now.yaml
Output:
1,150significant rows
18queries with hits
504GO terms
Output:
| query_id | query_name | significant_go_terms | unique_go_terms | best_adjusted_p | max_overlap |
|---|---|---|---|---|---|
| GSE11386_NAIVE_VS_MEMORY_BCELL_UP | gse11386 naive vs memory bcell up | 194 | 194 | 2.352e-50 | 191 |
| GSE11057_PBMC_VS_MEM_CD4_TCELL_UP | gse11057 pbmc vs mem cd4 tcell up | 176 | 176 | 2.705e-34 | 201 |
| GSE22886_NAIVE_VS_IGG_IGA_MEMORY_BCELL_DN | gse22886 naive vs igg iga memory bcell dn | 129 | 129 | 3.398e-48 | 200 |
| GSE10240_CTRL_VS_IL17_AND_IL22_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP | gse10240 ctrl vs il17 and il22 stim primary bronchial epithelial cells up | 85 | 85 | 2.016e-35 | 193 |
| NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP | nunoda response to dasatinib imatinib up | 80 | 80 | 1.925e-19 | 29 |
| GSE10325_LUPUS_BCELL_VS_LUPUS_MYELOID_UP | gse10325 lupus bcell vs lupus myeloid up | 78 | 78 | 3.842e-29 | 193 |
| RAPA_EARLY_UP.V1_UP | rapa early up.v1 up | 73 | 73 | 1.440e-27 | 168 |
| GSE7831_UNSTIM_VS_INFLUENZA_STIM_PDC_1H_UP | gse7831 unstim vs influenza stim pdc 1h up | 71 | 71 | 3.511e-42 | 204 |
| GSE9960_HEALTHY_VS_SEPSIS_PBMC_UP | gse9960 healthy vs sepsis pbmc up | 44 | 44 | 5.401e-36 | 190 |
| GSE18893_CTRL_VS_TNF_TREATED_TCONV_24H_UP | gse18893 ctrl vs tnf treated tconv 24h up | 36 | 36 | 4.000e-39 | 202 |
| GSE11864_UNTREATED_VS_CSF1_IFNG_IN_MAC_UP | gse11864 untreated vs csf1 ifng in mac up | 36 | 36 | 2.684e-33 | 199 |
| GSE10500_ARTHRITIC_SYNOVIAL_FLUID_VS_HEALTHY_MACROPHAGE_UP | gse10500 arthritic synovial fluid vs healthy macrophage up | 33 | 33 | 1.467e-30 | 152 |
| GSE16450_CTRL_VS_IFNA_12H_STIM_MATURE_NEURON_CELL_LINE_UP | gse16450 ctrl vs ifna 12h stim mature neuron cell line up | 29 | 29 | 2.391e-29 | 192 |
| GSE12366_NAIVE_VS_MEMORY_BCELL_UP | gse12366 naive vs memory bcell up | 28 | 28 | 2.856e-28 | 178 |
| BECKER_TAMOXIFEN_RESISTANCE_UP | becker tamoxifen resistance up | 25 | 25 | 1.330e-09 | 48 |
| GSE29614_CTRL_VS_DAY3_TIV_FLU_VACCINE_PBMC_UP | gse29614 ctrl vs day3 tiv flu vaccine pbmc up | 19 | 19 | 2.166e-20 | 164 |
| GSE11367_CTRL_VS_IL17_TREATED_SMOOTH_MUSCLE_CELL_UP | gse11367 ctrl vs il17 treated smooth muscle cell up | 11 | 11 | 5.400e-16 | 134 |
| GYORFFY_DOXORUBICIN_RESISTANCE | gyorffy doxorubicin resistance | 3 | 3 | 1.879e-04 | 35 |
Output:
The strongest unfiltered GO hits are often broad terms. For a more useful first look, the next table keeps terms with target size at most 500 genes.
Output:
| query_id | target_id | target_name | overlap | query_size | target_size | p_adjust_bonferroni |
|---|---|---|---|---|---|---|
| GSE11386_NAIVE_VS_MEMORY_BCELL_UP | GO:0051276 | chromosome organization | 28 | 191 | 424 | 1.218e-17 |
| GSE11386_NAIVE_VS_MEMORY_BCELL_UP | GO:0098687 | chromosomal region | 26 | 191 | 399 | 6.877e-16 |
| NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP | GO:0044772 | mitotic cell cycle phase transition | 11 | 29 | 130 | 5.338e-15 |
| NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP | GO:0044770 | cell cycle phase transition | 11 | 29 | 142 | 1.457e-14 |
| GSE11386_NAIVE_VS_MEMORY_BCELL_UP | GO:0098813 | nuclear chromosome segregation | 20 | 191 | 223 | 7.027e-14 |
| GSE11386_NAIVE_VS_MEMORY_BCELL_UP | GO:0000280 | nuclear division | 22 | 191 | 305 | 1.143e-13 |
| GSE11386_NAIVE_VS_MEMORY_BCELL_UP | GO:0007059 | chromosome segregation | 22 | 191 | 312 | 1.861e-13 |
| NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP | GO:0000307 | cyclin-dependent protein kinase holoenzyme complex | 9 | 29 | 66 | 2.760e-13 |
| GSE11386_NAIVE_VS_MEMORY_BCELL_UP | GO:0000793 | condensed chromosome | 21 | 191 | 278 | 2.986e-13 |
| NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP | GO:1902554 | serine/threonine protein kinase complex | 10 | 29 | 120 | 4.362e-13 |
| GSE11386_NAIVE_VS_MEMORY_BCELL_UP | GO:0048285 | organelle fission | 22 | 191 | 330 | 6.183e-13 |
| GSE10240_CTRL_VS_IL17_AND_IL22_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP | GO:0000775 | chromosome, centromeric region | 20 | 199 | 245 | 1.034e-12 |
| NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP | GO:1902911 | protein kinase complex | 10 | 29 | 134 | 1.362e-12 |
| NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP | GO:0000082 | G1/S transition of mitotic cell cycle | 9 | 29 | 79 | 1.526e-12 |
| NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP | GO:0044843 | cell cycle G1/S phase transition | 9 | 29 | 81 | 1.932e-12 |
| GSE10240_CTRL_VS_IL17_AND_IL22_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP | GO:0051983 | regulation of chromosome segregation | 18 | 199 | 185 | 2.341e-12 |
| GSE11057_PBMC_VS_MEM_CD4_TCELL_UP | GO:0002764 | immune response-regulating signaling pathway | 25 | 204 | 468 | 2.516e-12 |
| GSE11386_NAIVE_VS_MEMORY_BCELL_UP | GO:1901990 | regulation of mitotic cell cycle phase transition | 23 | 191 | 402 | 2.910e-12 |
| GSE11057_PBMC_VS_MEM_CD4_TCELL_UP | GO:0009897 | external side of plasma membrane | 23 | 204 | 392 | 7.395e-12 |
| GSE11386_NAIVE_VS_MEMORY_BCELL_UP | GO:0000775 | chromosome, centromeric region | 19 | 191 | 245 | 9.035e-12 |