Table 3.
Results from two different ranking functions of the interactome pipelinea.
| A | I | II | III | IV | |||
|---|---|---|---|---|---|---|---|
| Gene | Degree Rank | Betweenness Rank | De+Be Rank | ReRanking | Annotatiom | ||
| AFUA_6G11390 | 36 | 91 | 127 | 1 | 1,3-beta-glucanosyltransferase Gel2 | ||
| AFUA_5G01960 | 8 | 119 | 127 | 1 | Phosphate transporter (Pho88) | ||
| AFUA_1G09310 | 68 | 79 | 147 | 2 | DUF6 domain protein | ||
| AFUA_3G11070 | 52 | 96 | 148 | 3 | Pyruvate decarboxylase PdcA | ||
| AFUA_5G08420 | 124 | 55 | 179 | 4 | High osmolarity signaling protein Sho1 | ||
| AFUA_3G12800 | 137 | 60 | 197 | 5 | Clathrin-coated vesiclec protein (Bud7) | ||
| AFUA_2G10740 | 94 | 108 | 202 | 6 | Thiamin biosynthesis protein (Thi-4) | ||
| AFUA_5G12190 | 220 | 92 | 312 | 7 | Transcription initiation factor subunit (TAF30) | ||
| AFUA_4G09660 | 19 | 310 | 329 | 8 | Secretory component protein shr3 | ||
| AFUA_2G12230 | 261 | 135 | 396 | 9 | Mitochondrial large ribosomal subunit protein L16 | ||
| AFUA_6G12400 | 261 | 142 | 403 | 10 | 1,3-beta-glucan synthase catalytic subunit FksP | ||
| AFUA_3G12320 | 307 | 117 | 424 | 11 | Lipase/serine esterase | ||
| AFUA_1G06700 | 220 | 235 | 455 | 12 | Metacaspase CasA | ||
| AFUA_3G14140 | 220 | 235 | 455 | 12 | Metacaspase CasB | ||
| AFUA_4G13340 | 261 | 213 | 474 | 13 | DUF907 domain protein | ||
| AFUA_2G17650 | 261 | 213 | 474 | 13 | DUF907 domain protein | ||
| AFUA_2G17300 | 261 | 220 | 481 | 14 | Glutathione S-transferase | ||
| AFUA_1G17010 | 261 | 220 | 481 | 14 | Glutathione S-transferase | ||
| AFUA_2G09040 | 307 | 195 | 502 | 15 | Vacuolar transporter chaperone (Vtc4) | ||
| AFUA_2G04010 | 220 | 302 | 522 | 16 | Alpha, alpha-trehalose-phosphate synthase subunit | ||
| AFUA_6G12950 | 220 | 302 | 522 | 16 | Trehalose-phosphate synthase/phosphatase complex subunit Tps1, putative | ||
| B | I | II | III | ||||
| Gene | Priority order | New Rank (II+III) | RhumPDB RANK | Expression RANK | RhumPDB_score | Regulation, (Bertuzzi et al., 2014) | Annotation |
| AFUA_1G06940 | 1 | 11 | 1 | 10 | 183.000 | UP | Chorismate synthase |
| AFUA_3G04210 | 2 | 40 | 1 | 39 | 183.000 | – | Fatty acid synthase alpha subunit FasA |
| AFUA_2G10520 | 2 | 40 | 1 | 39 | 183.000 | – | Urate oxydase UaZ |
| AFUA_2G06230 | 3 | 41 | 2 | 39 | 180.716 | – | Glutamine amidotransferase:cyclase |
| AFUA_3G04220 | 4 | 43 | 4 | 39 | 178.380 | – | Fatty acid synthase beta subunit |
| AFUA_3G09290 | 5 | 52 | 13 | 39 | 149.637 | – | Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent |
| AFUA_6G04700 | 5 | 52 | 37 | 15 | 71.699 | UP | Imidazoleglycerol-phosphate dehydratase |
| AFUA_3G06830 | 6 | 55 | 16 | 39 | 142.097 | – | Aspartate-semialdehyde dehydrogenase |
| AFUA_1G14570 | 7 | 57 | 18 | 39 | 122.634 | – | Phosphoribosyl-AMP cyclohydrolase |
| AFUA_5G06160 | 8 | 66 | 27 | 39 | 93.000 | – | 5-proFAR isomerase His6 |
| AFUA_5G13130 | 9 | 77 | 38 | 39 | 70.079 | – | Chorismate mutase |
| AFUA_2G10740 | 10 | 85 | 46 | 39 | 54.176 | – | Thiamin biosynthesis protein (Thi-4) |
| AFUA_4G06460 | 10 | 85 | 83 | 2 | 5.301 | UP | Pentafunctional AROM polypeptide |
| AFUA_3G14490 | 11 | 94 | 55 | 39 | 46.813 | – | Ketol-acid reductoisomerase |
| AFUA_5G05590 | 12 | 102 | 48 | 54 | 52.301 | DOWN | Aspartokinase |
| AFUA_1G05530 | 13 | 105 | 60 | 45 | 39.523 | DOWN | Uridine nucleosidase Urh1 |
| AFUA_5G05820 | 13 | 105 | 66 | 39 | 25.362 | – | Homoserine kinase |
| AFUA_4G04030 | 14 | 109 | 70 | 39 | 14.660 | – | Histidinol-phosphatase |
| AFUA_4G11980 | 15 | 114 | 63 | 51 | 33.665 | DOWN | Anthranilate phosphoribosyltransferase |
| AFUA_6G12400 | 16 | 140 | 101 | 39 | −0.513 | – | 1,3-beta-glucan synthase catalytic subunit FksP |
| AFUA_4G13680 | 17 | 167 | 117 | 50 | −5000.000 | DOWN | Phosphatidylserine synthase |
List of promising targets from two different ranking procedures. Table (A) describes the results of the first ranking calculation considering the genes degree rank (A.I) as well as its subsequent betweenness rank in the metabolic pathway (A.II). The added values from (A.I) and (A.II) are listed in (A.III). (A.IV) contains the re-ranking based on column (A.III). Table (B) proceeds with calculation of a RhumPDB Rank (B.II), an expression rank (B.III, Bertuzzi et al., 2014) and a final addition of those two values, leading to the new ranking (B.I). The resulting order illustrates the priority of the target in context with the metabolic function, the expression and the three dimensional structure of the protein. For detailed description see Materials and Methods.