Table II. Representative studies using functional protein microarrays.
| Classification/Research | Tools | Major findings | Refs. |
|---|---|---|---|
| Protein-Protein | |||
| Calmodulin | Yeast proteome array | Identified 30 new targets | (3) |
| 4 antimicrobial peptides | E. coli proteome array | Identified many intracellular targets | (35) |
| 2-oxohistidine peptide | E. coli proteome array | Identified 9 redox targets | (112) |
| NS5A | HuProt | Identified 90 targets and validated Pim1 | (44) |
| PknG | HuProt | Identified 125 targets and validated CypA | (47) |
| MTB proteome array | Identified 59 targets | (7) | |
| ROP18 | HuProt | Identified 68 targets and validated 4 bindings | (46) |
| SidM, LidA, and AnkX | Human NAPPA | Identified 18, 20, and 8 host targets | (48, 49) |
| 61 ErbB peptides | SH2 PBD array | Profiled interaction networks | (20) |
| Protein-Lipid | |||
| 5 Phospholipids | Yeast proteome array | Identified 150 targets | (3) |
| Protein-Cell/Lysate | |||
| HBMEC | E. coli proteome array | Identified 23 targets and validated YojI | (38) |
| Macrophage lysate | MTB proteome array | Identified 26 targets | (113) |
| Small Molecule Binding | |||
| 2 inhibitors of rapamycin | E. coli proteome array | Identified 39 targets and validated Tep1p and Nir1p | (29) |
| Arsenic | HuProt | Identified 360 targets and validated hexokinase | (53) |
| 6-O-angeloylplenolin | HuProt | Identified 99 targets and validated STAT3 | (54) |
| Cyclic di-GMP | MTB proteome array | Identified 30 targets | (7) |
| E. coli proteome array | Identified 8 targets and validated CobB | (37) | |
| Substrate Identification | |||
| Six SUMO E3 ligases | HuProt | Identified 250 substrates and validated PYK2 | (114) |
| 289 kinases | HuProt ver. I | Constructed a high resolution kinase-substrate network | (115) |
| Four herpesvirus kinases | HuProt | Identified a conserved host pathway for viral replication | (116) |
| ppGalNAc-Ts | HuProt | Identified 128 common substrates for glycosylation | (51) |
| VopS and IbpAFic2 | Human NAPPA | Identified 21 AMPylation substrates | (52) |
| 87 yeast kinases | Yeast proteome array | Constructed a kinase-substrate network | (117) |
| Ubiquitin E3 Rsp5 | Yeast proteome array | Identified 84 substrates and validated Rnr2 | (33) |
| NuA4 | Yeast proteome array | Discovered two yeast ageing pathways involving Pck1p and Sip2 | (32, 118) |
| Tyrosine sulfation | E. coli proteome array | Identified 875 substrates | (40) |
| 11 MTB kinases | MTB proteome array | Identified 1,027 interaction network | (58) |
| Protein-DNA | |||
| Yeast genomic DNA | Yeast proteome array | Identified 200 targets and validated Arg5,6 | (30) |
| Mismatch and abasic site | E. coli proteome array | Validated YbaZ and YbcN | (8) |
| Promoter DNA of fimS | E. coli proteome array | Identified 19 targets and validated Spr | (34) |
| 460 DNA motifs | 4,191 human array | Discovered many unconventional DNA-binding proteins and showed Erk2 as a transcriptional repressor | (12) |
| Protein-RNA | |||
| BMV viral RNA | Yeast proteome array | Identified and validated Pus4 and App1's role in preventing viral spreading in tobacco | (31) |
| 13 IncRNAs | HuProt | Found many unconventional RNA-binding proteins and validated IDH1 | (42) |
| miR-122 | HuProt | Identified 40 targets and validated hnRNP K | (43) |
| Antibody specificity | |||
| mAbs against TFs | HuProt | Demonstrated the use of HuProt for specificity test of mAbs | (57) |
| 400 Abs against SH2 | SH2 PrESTs array | Verified Abs specificity | (111) |
mAbs = monoclonal antibodies.