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

Söderholm, Sandra; Hintsanen, Petteri; Öhman, Tiina; Aittokallio, Tero; Nyman, Tuula A

doi:10.1186/1477-5956-12-36

Proteome Science

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

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.

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ISSN: 1477-5956

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