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Table 2 Ingenuity pathway analysis (IPA)

From: Transcriptome-wide study of TNF-inhibitor therapy in rheumatoid arthritis reveals early signature of successful treatment

Top canonical pathways
 Name p value Overlap
  Altered T cell and B cell signalling in rheumatoid arthritis 1.41E− 10 17.3%, 14/81
  TREM1 signalling 2.53E− 10 18.6%, 13/70
  Dendritic cell maturation 5.68E− 08 9.5%, 16/169
  Allograft rejection signalling 1.39E− 07 18.8%, 9/48
  Communication between innate and adaptive immune cells 2.06E− 07 13.4%, 11/82
Top upstream regulators
 Upstream regulator p value of overlap
  TGM2 4.66E− 15
  CEBPA 1.16E− 08
  CSF2 1.70E− 08
  TNF 1.53E− 06
  IRF4 2.33E− 06
Top diseases and disorders
 Name p value Molecules
  Immunological disease 6.30E− 03 to 1.20E− 22 151
  Connective tissue disorders 5.32E− 03 to 3.31E− 21 81
  Inflammatory disease 6.18E− 03 to 3.31E− 21 116
  Skeletal and muscular disorders 5.32E− 03 to 3.31E− 21 106
  Infectious diseases 5.76E− 03 to 5.84E− 20 76
Top molecular and cell functions
 Name p value Molecules
  Cell-to-cell signalling and interaction 6.18E− 03 to 1.99E− 14 100
  Cell death and survival 7.09E− 03 to 3.79E− 10 97
  Cellular movement 6.44E− 03 to 4.26E− 10 55
  Cellular development 6.48E− 03 to 5.54E− 10 49
  Cellular growth and proliferation 6.18E− 03 to 5.54E− 10 84
Top physiological system development and function
 Name p value Molecules
  Haematological system development and function 6.48E− 03 to 6.44E− 13 72
  Immune cell trafficking 6.18E− 03 to 6.44E− 13 47
  Embryonic development 1.86E− 05 to 1.86E− 05 4
  Haematopoiesis 6.48E− 03 to 2.86E− 05 24
  Hair and skin development and function 6.18E− 03 to 4.26E− 05 10
  1. The differentially expressed genes in adalimumab good-responders (baseline versus 3 months) were analysed using Ingenuity Pathway Analysis (IPA) software. The top associated terms for the output themes, which were either up- or downregulated, are presented with associated p values. The table also displays the number of molecules, or the number of differentially expressed transcripts within the dataset associated with each term