Table 2.
KEGG pathways that were up-regulated and down-regulated in FCHL patients compared with controls
| Name | Size | ES | NES | NOM P value | FDR q value | FWER P value | Rank at max |
|---|---|---|---|---|---|---|---|
| KEGG pathways that are up-regulated in FCHL (FDR q value <0.05) | |||||||
| HSA04612_antigen_processing_and_presentation | 36 | 0.7782 | 2.85797 | 0 | 1 E-30 | 0 | 925 |
| HSA04514_cell_adhesion_molecules | 56 | 0.6689 | 2.67752 | 0 | 1 E-30 | 0 | 1597 |
| HSA04610_complement_and_coagulation_cascades | 19 | 0.7961 | 2.41627 | 0 | 1 E-30 | 0 | 1191 |
| HSA04940_type_1_diabetes_mellitus | 23 | 0.7214 | 2.36695 | 0 | 2.15E-04 | 0.001 | 1480 |
| HSA04640_hematopoietic_cell_lineage | 22 | 0.7116 | 2.30842 | 0 | 1.72E-04 | 0.001 | 1557 |
| HSA04512_ECM_receptor_interaction | 42 | 0.5952 | 2.26881 | 0 | 1.43E-04 | 0.001 | 1017 |
| HSA04060_cytokine_cytokine_receptor_interaction | 63 | 0.5239 | 2.17418 | 0 | 6.86E-04 | 0.005 | 1526 |
| HSA01032_glycan_structures_degradation | 17 | 0.7017 | 2.12834 | 0 | 0.00123 | 0.01 | 2025 |
| HSA01430_cell_communication | 36 | 0.5845 | 2.10512 | 0 | 0.00121 | 0.011 | 1660 |
| HSA04670_leukocyte_transendothelial_migration | 58 | 0.5201 | 2.10461 | 0 | 0.001089 | 0.011 | 1999 |
| HSA04650_natural_killer_cell_mediated_cytotoxicity | 60 | 0.5008 | 2.02132 | 0 | 0.002171 | 0.024 | 1599 |
| HSA00511_N_glycan_degradation | 10 | 0.7608 | 1.96087 | 0.0042 | 0.00408 | 0.048 | 2025 |
| HSA03010_ribosome | 63 | 0.4611 | 1.88859 | 0 | 0.006919 | 0.086 | 3519 |
| HSA04360_axon_guidance | 64 | 0.4502 | 1.84904 | 0.0021 | 0.009319 | 0.123 | 1904 |
| HSA04510_focal_adhesion | 119 | 0.3698 | 1.69301 | 0 | 0.035797 | 0.427 | 1017 |
| KEGG pathways that are down-regulated in FCHL (FDR q value <0.05) | |||||||
| HSA00280_valine_leucine_and_isoleucine_degradation | 34 | −0.6564 | −23340 | 0.0 | 1 E-30 | 0.0 | 1577 |
| HSA00640_propanoate_metabolism | 25 | −0.6194 | −20359 | 0.001879 | 0.00747 | 0.015 | 1577 |
| HSA00650_butanoate_metabolism | 25 | −0.5745 | −18970 | 0.00185 | 0.02188 | 0.061 | 1577 |
| HSA00020_citrate_cycle | 24 | −0.5928 | −18958 | 0.0 | 0.01669 | 0.062 | 3091 |
| HSA01040_polyunsaturated_fatty_acid_biosynthesis | 12 | −0.70587 | −18875 | 0.0 | 0.01459 | 0.068 | 1431 |
| HSA00030_pentose_phosphate_pathway | 14 | −0.6339 | −1.663 | 0.001855 | 0.0462 | 0.235 | 1609 |
Pathways that are significant at an FDR of 5% or less are listed. Column headings are as follows: name, name of the KEGG pathway; size, number of genes contained in the pathways; ES, enrichment score (a measure of the extent to which a pathway is overrepresented at the top or bottom of a ranked list of genes); NES, normalized enrichment score, after adjustment for pathway size; NOM P value, nominal P value obtained from gene-set level permutations; FDR q value, FDR to correct for multiple testing; FWER P value, family-wise error rate correction for multiple testing; rank at max, the position in the ranked gene list at which maximum enrichment of the pathway was observed. Nominal P < 0.001 values and FDR q < 0.0001 values are listed as zeros.