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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.