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Table 3 Top associated Gene Ontologies with the anti-TNF response at baseline and week 20 and with the longitudinal change

From: Lower peripheral helper T cell levels in the synovium are associated with a better response to anti-TNF therapy in rheumatoid arthritis

GOs associated with differential expression: week 0
ID Description Count P value Gene group
GO:0044772 Mitotic cell cycle phase transition 75 3.64e−17 Non-response
GO:0044770 Cell cycle phase transition 77 1.07e−16 Non-response
GO:0140014 Mitotic nuclear division 47 2.39e−13 Non-response
GO:0000280 Nuclear division 56 3.70e−12 Non-response
GO:0051301 Cell division 70 1.81e−11 Non-response
GO:0007346 Regulation of mitotic cell cycle 71 2.04e−11 Non-response
GO:0048285 Organelle fission 57 4.90e−11 Non-response
GO:0000070 Mitotic sister chromatid segregation 31 5.86e−11 Non-response
GO:0000819 Sister chromatid segregation 33 3.24e−10 Non-response
GOs associated with differential expression: week 20
GO:0043299 Leukocyte degranulation 40 3.97e−11 Non-response
GO:0042119 Neutrophil activation 38 1.07e−10 Non-response
GO:0036230 Granulocyte activation 38 1.46e−10 Non-response
GO:0002275 Myeloid cell activation involved in immune response 39 3.61e−10 Non-response
GO:0002444 Myeloid leukocyte mediated immunity 39 6.36e−10 Non-response
GOs associated with longitudinal change in responders
Gene Ontology Description Count P value Gene group
GO:0043299 Leukocyte degranulation 74 3.24e−32 Downregulated
GO:0002275 Myeloid cell activation involved in immune response 74 1.14e−31 Downregulated
GO:0002444 Myeloid leukocyte mediated immunity 73 2.99e−30 Downregulated
GO:0036230 Granulocyte activation 68 1.40e−28 Downregulated
GO:0042119 Neutrophil activation 67 5.88e−28 Downregulated
GO:0002283 Neutrophil activation involved in immune response 65 1.18e−26 Downregulated
GO:0002446 Neutrophil mediated immunity 65 5.17e−26 Downregulated
GO:0043312 Neutrophil degranulation 64 5.65e−26 Downregulated
GO:0030198 Extracellular matrix organization 53 4.20e−16 Upregulated
GO:0043062 Extracellular structure organization 53 4.01e−13 Upregulated
GO:0009617 Response to bacterium 50 1.64e−11 Downregulated
GO:0002764 Immune response-regulating signaling pathway 45 2.69e−11 Downregulated
GO:0002757 Immune response-activating signal transduction 42 2.06e−10 Downregulated
GO:0002250 Adaptive immune response 39 2.23e−10 Downregulated
GO:0045088 Regulation of innate immune response 37 6.63e−10 Downregulated
GO:0001501 Skeletal system development 54 7.19e−10 Upregulated
  1. List of the most significantly associated (P < 1e−9, multiple test adjusted) Gene Ontologies in the three pathway level analyses based on three analyses: (i) genes differentially expressed in the synovial membrane between anti-TNF responders and non-responders at baseline, (ii) genes differentially expressed between anti-TNF responders and non-responders at week 20, and (iii) genes differentially expressed between week 0 and week 20 in the anti-TNF responder group
  2. ID Gene Ontology ID, Count number of differentially expressed genes that belong to the GO, P value significance of the observed enrichment (Bonferroni-corrected for the number of total GOs tested), Gene Group differential expression group from which the genes were selected to test for enrichment