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Table 2 The STRING analysis of the AD specific protein network where corrected difference in observation frequency and the Chi Square value were both greater than 15 that showed: nodes, 1248; number of edges, 5604; average node degree, 8.98; avg. local clustering coefficient, 0.321; expected number of edges, 5362; PPI enrichment p-value, 0.000516

From: The plasma peptides of Alzheimer’s disease

Term ID Term description Observed gene count Background gene count False discovery rate
KW-0025 Alternative splicing 821 10223 1.98E-18
KW-0963 Cytoplasm 379 4972 0.0178
GO:0005829 cytosol 405 4958 0.0000291
GO:0044444 cytoplasmic part 695 9377 0.0000291
GO:0005737 Cytoplasm 809 11238 0.0000436
GO:0005622 Intracellular 983 14286 0.0007
GO:0044424 Intracellular part 966 13996 0.0007
GO:0043226 Organelle 866 12432 0.0022
GO:0005623 Cell 1092 16271 0.0029
GO:0044464 Cell part 1090 16244 0.003
GO:0043229 Intracellular organelle 848 12193 0.0034
GO:0043231 Intracellular membrane-bounded organelle 729 10365 0.0096
GO:0044422 Organelle part 649 9111 0.0096
GO:0005768 Endosome 85 876 0.0158
GO:0043227 Membrane-bounded organelle 781 11244 0.0158
GO:0098576 Lumenal side of membrane 9 29 0.0219
GO:0055037 Recycling endosome 24 164 0.024
GO:0044446 Intracellular organelle part 627 8882 0.0287
GO:0071556 Integral component of lumenal side of endoplasmic reticulum 8 26 0.0404
GO:0003824 Catalytic activity 435 5592 0.0028
GO:0005488 Binding 830 11878 0.0174
GO:0008152 Metabolic process 696 9569 0.0108
GO:0051726 Regulation of cell cycle 115 1129 0.0108
GO:0010564 Regulation of cell cycle process 76 684 0.0175
GO:1901990 Regulation of mitotic cell cycle phase transition 47 351 0.0175
GO:0045786 Negative regulation of cell cycle 61 517 0.0186
GO:0010821 Regulation of mitochondrion organization 26 148 0.0187
GO:0044237 Cellular metabolic process 637 8797 0.0187
GO:0044238 Primary metabolic process 638 8808 0.0187
GO:0071704 Organic substance metabolic process 657 9135 0.0187
GO:1901987 Regulation of cell cycle phase transition 49 385 0.0187
GO:0008104 Protein localization 172 1966 0.0208
GO:0007346 Regulation of mitotic cell cycle 67 608 0.0212
GO:0006807 Nitrogen compound metabolic process 603 8349 0.0286
GO:0009056 Catabolic process 162 1859 0.0286
GO:0009987 Cellular process 994 14652 0.0286
GO:0010823 Negative regulation of mitochondrion organization 13 50 0.0286
GO:0044248 Cellular catabolic process 147 1646 0.0286
GO:0048583 Regulation of response to stimulus 306 3882 0.0286
GO:0051641 Cellular localization 186 2180 0.0286
GO:0080134 Regulation of response to stress 120 1299 0.0286
GO:0097190 Apoptotic signaling pathway 39 295 0.0286
GO:1901564 Organonitrogen compound metabolic process 401 5281 0.0286
GO:0032270 Positive regulation of cellular protein metabolic process 134 1496 0.0315
GO:0019538 Protein metabolic process 324 4194 0.0389
GO:0044403 Symbiont process 68 650 0.0389
GO:0007093 Mitotic cell cycle checkpoint 24 153 0.0434
GO:0044260 Cellular macromolecule metabolic process 472 6413 0.0434
GO:0016032 Viral process 61 571 0.0439
GO:0016197 Endosomal transport 27 185 0.0452
GO:0051128 Regulation of cellular component organization 191 2306 0.0452
GO:0051247 Positive regulation of protein metabolic process 139 1587 0.0452
GO:0043170 Macromolecule metabolic process 539 7453 0.0463
  1. Keywords, GO components, processes and functions from STRING analysis of gene symbols with a χ2 ≥ 25 for AD versus AD control
  2. The supporting information from the STRING analysis may be found in Additional files 2, 3, 4: Table S2–S4
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Clinical Proteomics

ISSN: 1559-0275