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Table 1 Proteins with a degree ≥ 30 in the dynamics-based network.

From: Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data

IPI accession

Degree

Biological process

IPI00002591

45

phosphatidylinositol biosynthetic process; receptor-mediated endocytosis; phosphoinositide phosphorylation; phosphoinositide-mediated signaling

IPI00294391

44

regulation of cell shape; signal transduction

IPI00438229

43

epithelial to mesenchymal transition; regulation of transcription from RNA polymerase II promoter; positive regulation of gene-specific transcription

IPI00148057

42

cell surface receptor linked signal transduction; chromatin modification; regulation of transcription from RNA polymerase II promoter; regulation of growth

IPI00291916

42

insulin receptor signaling pathway

IPI00000858

40

regulation of transcription, DNA-dependent

IPI00299263

40

intracellular protein transport; protein secretion; vesicle-mediated transport; regulation of ARF GTPase activity

IPI00093253

39

double-strand break repair via homologous recombination

IPI00009975

39

regulation of transcription, DNA-dependent

IPI00003406

38

regulation of dendrite development; actin filament organization; regulation of neuronal synaptic plasticity

IPI00170770

37

multicellular organismal development; transcription

IPI00550206

37

regulation of transcription, DNA-dependent

IPI00017030

37

anti-apoptosis

IPI00464952

36

nuclear mRNA splicing, via spliceosome

IPI00010141

36

DNA replication

IPI00552897

36

DNA repair; cell cycle

IPI00026673

35

multicellular organismal development; negative regulation of transcription from RNA polymerase II promoter

IPI00298731

35

protein import into nucleus; transcription

IPI00425404

35

microtubule-based movement

IPI00217957

34

multicellular organismal development; transcription

IPI00438170

34

protein transport; cell communication

IPI00097495

34

regulation of Rab GTPase activity

IPI00021954

33

retrograde vesicle-mediated transport, Golgi to ER; COPI coating of Golgi vesicle; regulation of ARF protein signal transduction

IPI00298935

33

oxidation reduction; chromatin modification; regulation of transcription, DNA-dependent

IPI00414262

32

activation of JUN kinase activity

IPI00181006

32

regulation of transcription, DNA-dependent; apoptosis

IPI00004472

32

protein amino acid phosphorylation; protein kinase cascade; ion transport

IPI00431698

32

interspecies interaction between organisms; regulation of transcription, DNA-dependent

IPI00004233

32

cell proliferation; cell cycle

IPI00296388

31.33

regulation of transcription, DNA-dependent; chromatin remodeling

IPI00219430

30

transcription initiation from RNA polymerase II promoter; androgen receptor signaling pathway; regulation of transcription, DNA-dependent

IPI00301503

30

RNA splicing, via transesterification reactions; nuclear mRNA splicing, via spliceosome

  1. Here, "Node degree" indicates the mean degree of phosphopeptides of the corresponding protein in the dynamics-based network with R > 0.99. The biological process represents the result annotated by means of gene ontology, as described in the Methods section.
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BMC Bioinformatics

ISSN: 1471-2105

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