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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