Table 2.
Main hub partners of common neurodegeneration-associated proteins.
| Gene symbol | Protein ID | Protein partners | ND-associated protein partners | Enrichment factor | Adjusted p-value |
|---|---|---|---|---|---|
| TRAF6 | Q9Y4K3 | 315 | 17 | 28.40 | 1.03E-17 |
| PRKN | O60260 | 454 | 18 | 20.86 | 2.77E-16 |
| SQSTM1 | Q13501 | 309 | 13 | 22.14 | 8.25E-13 |
| HSPA4 | P34932 | 363 | 13 | 17.90 | 1.58E-10 |
| HSPA8 | P11142 | 708 | 16 | 11.29 | 8.20E-10 |
| YWHAZ | P63104 | 412 | 12 | 14.56 | 9.38E-9 |
| HSP90AA1 | P07900 | 839 | 15 | 8.93 | 6.65E-08 |
| YWHAQ | P27348 | 476 | 11 | 11.55 | 4.74E-07 |
| CYLD | Q9NQC7 | 620 | 12 | 9.67 | 8.15E-07 |
| CTNNB1 | P35222 | 616 | 11 | 8.92 | 6.00E-06 |
| UBC | P0CG48 | 1050 | 14 | 6.66 | 6.54E-06 |
| TP53 | P04637 | 1062 | 14 | 6.59 | 7.46E-06 |
| CUL7 | Q14999 | 658 | 11 | 8.35 | 1.13E-05 |
| EGFR | P00533 | 1224 | 14 | 5.71 | 3.73E-05 |
| RNF4 | P78317 | 1251 | 14 | 5.59 | 4.75E-05 |
| MCM2 | P49736 | 940 | 11 | 5.85 | 3.09E-04 |
| BRCA1 | P38398 | 962 | 11 | 5.71 | 3.80E-04 |
| NTRK1 | P04629 | 1948 | 16 | 4.10 | 4.54E-04 |
| CUL3 | Q13618 | 1227 | 13 | 5.29 | 1.75E-04 |
| ESR2 | Q92731 | 2249 | 13 | 2.89 | 4.67E-02 |
A survey of the human proteome was performed by querying the protein-protein interaction database BioGRID (38). Candidate hub proteins interacting with more than 10 common neurodegeneration-associated proteins were retrieved. The lists of partners currently demonstrated for each of these candidate hubs were then retrieved. For each of these lists, a factor of enrichment in neurodegeneration-associated proteins was established along with an associated Fisher's exact test p-value, as described in the Materials and Methods section. From left to right, gene symbols and corresponding protein IDs of the identified hub proteins are shown in the first and second column, the associated total numbers of partners and total numbers of neurodegeneration (ND)-associated protein interactors are shown in the third and fourth column. The corresponding enrichment factors and adjusted p-values are shown in the last two columns. Enrichment factors and statistical analyses were performed on data retrieved from the 3.5.175 release of BioGrid or, for PRKN, SQSTM1 and TRAF6, from the 3.5.177 release of BioGrid. Proteins that are detectable by mass spectrometry in human B lymphocytes, according to the “Human Proteome Map” database (39), are highlighted in gray.