Table 2. Top 8 tight clusters and functional enrichment.
| Cluster | Proteins (traced back from phosphopeptides) | Enriched terms |
| 1 | YRO2, BUG1, VPS74, HXK1, PIL1, FBP26, PTK2, NPA3, BIR1, MYO3, UTP14, ARE2, DBP5, RUD3 | Nucleotide phosphate-binding region:ATP (P-value = 6.54E-04, Benjamini = 3.4E-2) ** |
| Nucleotide-binding (P-value = 1.8E-3, Benjamini = 4.2E-2) ** | ||
| ATP-binding (P-value = 6.0E-3, Benjamini = 9.3E-2) * | ||
| 2 | VMA2, SEC31, GLY1, PEA2, VTC2, KEM1, UFD1, TIF4631, BCY1, SPA2, MFT1, NEW1, KRE6 | - |
| 3 | NUP60, SLA1, STU1, YCL020W, VBA4, HOM2, YDR365W-B, VPS74, PSP1, CHD1, NUP145, SPT6, HSE1, ABF1, MEH1, CKI1, YLR413W, SPT5, HRB1, LCB4, CAF20, MRL1 | Endosome (P-value = 1.6E-3, Benjamini = 6.6E-2) * |
| RNA polymerase II transcription elongation factor activity (P-value = 1.4E-3, Benjamini = 9.6E-2) * | ||
| Transcription elongation regulator activity (P-value = 2.8E-3, Benjamini = 9.9E-2) * | ||
| 4 | FAP7, ITR1, LSB3, LEU1, FLC3, SPT6, YGR125W, CRP1, KEL1, LCB3, YBT1, BDF1, YMR031C, DDR48, YMR295C, GPD2, ZEO1, CAF20, SNF2 | - |
| 5 | PIN4, CYC8, BUD3, LYS20, CDC34, MAK21, BFR2, SUM1, GLY1, NUP145, PRP43, SPT6, ENP2, YOR1, SSZ1, NUP2, YLR345W, SUB1, ESC1, BDP1, DCP2, RPC31, SLA2, NOP8, ALE1, MSB1, SNU66 | Nucleus (P-value = 1.0E-4, Benjamini = 3.4E-3) *** |
| Nuclear lumen (P-value = 3.4E-4, Benjamini = 2.7E-2) ** | ||
| 6 | SIF2, PPH22, VAC8, HSP12, RTF1, RSC30, TRA1, LCB3, NAP1, SIC1, RPN13, YMR196W, MRE11, MCK1, LEM3, FPK1, LSP1 | - |
| 7 | IST2, AIM3, RPC53, YDR186C, ECM32, MIG1, HXK2, VHS2, RNR2, UTR1, FBA1, EAP1, YLR257W, PFK2, PFK2, ACC1, YOR052C | Fructose and mannose metabolism (P-value = 3.0E-3, Benjamini = 3.9E-2) ** |
| Glycolysis (P-value = 1.6E-3, Benjamini = 4.3E-2) ** | ||
| Glycolysis/gluconeogenesis (P-value = 9.8E-3, Benjamini = 6.2E-2) * | ||
| 8 | AKL1, IST2, MAK5, FEN1, LHP1, RPC53, SAS10, SHS1, MAK21, DOP1, GCD6, GUK1, CHO1, PDA1, LEU1, NOP7, SPT6, TFG1, HXT1, AIM21, URA2, CDC11, MAK11, VPS13, CBF5, VTA1, CRN1, YMR031C, EFR3, ADE4, NOP12, MAM3, CAF20, PEX25, TIF5 | Ribosome biogenesis (P-value = 1.0E-4, Benjamini = 5.0E-3) *** |
Functional enrichment P-value and Benjamini-Hochberg corrected p-value (Benjamini) were calculated with DAVID Functional Annotation Tool [33], [34]. They are given in the brackets following corresponding terms.
*
Benjamini <0.1,
**
Benjamini <0.05,
***
Benjamini <0.01.
All the clusters are highly enriched in the term “phosphoprotein” (not listed above).