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Table 3 Enriched functional terms and canonical pathways, identified using DAVID and ingenuity pathway analysis (IPA)

From: ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining

Category Term or pathway P-value
Promoter
 SP_PIR_KEYWORDS Transcription regulation 2.00E-08
 GOTERM_MF Transcription regulator activity 6.72E-06
 GOTERM_BP Regulation of transcription from RNA polymerase II promoter 8.83E-06
 GOTERM_MF Transcription factor activity 2.56E-05
 SP_PIR_KEYWORDS Phosphoprotein 5.31E-05
 SP_PIR_KEYWORDS DNA-binding 9.99E-05
 GOTERM_BP Regulation of RNA metabolic process 1.31E-04
 GOTERM_BP Positive regulation of transcription 1.43E-04
 SP_PIR_KEYWORDS Developmental protein 1.56E-04
 SP_PIR_KEYWORDS Activator 1.85E-04
 SP_PIR_KEYWORDS Repressor 2.61E-04
 Canonical pathwaya Role of NFAT in cardiac Hypertrophy 4.36E-06
Wnt/β-catenin signalling 2.42E-04
Molecular Mechanisms of Cancer 3.91E-04
cAMP-mediated signalling 5.60E-04
Dopamine-DARPP32 Feedback in cAMP signalling 6.05E-04
Gene body
 GOTERM_MF DNA binding 1.82E-07
 INTERPRO IPR001766:Transcription factor, fork head 3.34E-06
 GOTERM_MF Sequence-specific DNA binding 9.11E-06
 SP_PIR_KEYWORDS Developmental protein 9.66E-06
 GOTERM_MF Transcription regulator activity 4.65E-05
 GOTERM_MF Transcription factor activity 9.25E-05
 SP_PIR_KEYWORDS Transcription regulation 1.62E-04
 Canonical pathwaya Notch signalling 4.89E-05
  1. Only annotations with P < 0.02 after Benjamini-Hochberg correction for multiple hypothesis testing are presented. Full lists and more details are provided in Additional file 5: Table S1 and S2
  2. aCanonical pathways were outputs from IPA analysis; other significant functional annotation terms were obtained from DAVID analysis