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Table 1 Top-ranked canonical pathways and networks after dsRNA-stimulation of human keratinocytes and control samples

From: PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data

A.    
Manual compilation   PhosFox  
Pathways p-value   p-value
Role of BRCA1 in DNA damage 0.0018 DNA methylation and transcriptional repression signaling 0.0012
Cell cycle: G2/M DNA damage checkpoint regulation 0.0061 Cyclins and cell cycle regulation 0.0027
Mismatch repair in eukaryotes 0.0082 Role of BRCA1 in DNA damage 0.0031
Phosphatidylethanolamine biosynthesis III 0.0087 Endometrial cancer signaling 0.0085
DNA damage-induced 14-3-3σ signaling 0.012 ATM signaling 0.013
Networks score   score
Cell death and survival, cell cycle, nervous system development and function 21 Cellular assembly and organization, cellular compromise, cell death and survival 36
Cell cycle, DNA replication, recombination and repair, cell death and survival 19 Gene expression, cell signaling, post-translational modification 34
RNA post-transcriptional modification, cell morphology, cellular compromise 19 Cell cycle, cellular movement, gene expression 17
B.    
Manual compilation   PhosFox  
Pathways p-value   p-value
ATM signaling 1.25E-04 Epithelial adherens junction signaling 5.65E-06
GADD45 signaling 4.85E-04 Remodeling of epithelial adherens junctions 1.26E-04
DNA damage-induced 14-3-3σ signaling 4.85E-04 Sertoli cell-sertoli cell junction signaling 1.78E-04
Role of CHK proteins in cell cycle checkpoint control 1.1E-03 ATM signaling 3.80E-04
Cell cycle: G2/M DNA damage checkpoint regulation 5.34E-03 Germ cell-sertoli cell junction signaling 8.43E-04
Networks score   score
Cell cycle, DNA replication, recombination, and repair, gene expression 45 Cell morphology, cellular function and maintenance, cell cycle 39
RNA post-transcriptional modification, cell cycle, cellular movement 21 Cellular assembly and organization, DNA replication, recombination, and repair, cell morphology 37
Cellular development, cellular movement, connective tissue disorders 19 Organismal survival, organ morphology, respiratory system development and function 37
  1. The IPA top-ranked canonical pathways and networks for the manually compiled and PhosFox-processed dsRNA-stimulated datasets (A) and control datasets (B) of the qualitative phosphoproteomic case study example.