TABLE 1.
Proteins differentially correlated in Cucumis sativus co-expression networks (Fe sufficiency, Mo sufficiency, Fe starvation, and Mo starvation).
| Annotation |
LDA |
Degree |
Function | |||||||||
| UNIPROT ID (C. sativus) | Gene name C. sativus | Gene name A. thaliana | Homology | Score | F Ratio | Prob > F | +Fe | +Mo | −Fe | −Mo | ||
| (A) | A0A0A0K4Q8 | Csa_7G073600 | MCCB (AT4G34030) | 77% | 918 | 11,1 | 1,1E-04 | 55 | 5 | 2 | 9 | Methylcrotonyl-CoA carboxylase, subunit beta |
| A0A0A0LM23 | Csa_2G382440 | FLOT1 (AT5G25250) | 75% | 723 | 4,6 | 1,2E-02 | 51 | Flotilins-like | ||||
| A0A0A0LXD4 | Csa_1G424875 | AT4G30010 | 69% | 142 | 42 | 1 | 2 | 8 | ATP-dependent RNA helicase | |||
| A0A0A0L0B9 | Csa_4G082380 | MBL1 (AT1G78850) | 50% | 434 | 3,9 | 2,1E-02 | 39 | Mannose-binding lectin | ||||
| A0A0A0K5L0 | Csa_7G387180 | MCCA (AT1G03090) | 69% | 1023 | 38 | 4 | 3 | 10 | Methyl crotonyl-CoA carboxylase subunit alpha | |||
| A0A0A0KJ29 | Csa_6G526470 | AT3G58140 | 74% | 657 | 36 | Phenylalanyl-tRNA synthetase | ||||||
| A0A0A0KCX8 | Csa_6G077980 | ARGAH1 (AT4G08900) | 85% | 590 | 34 | 1 | 0 | 4 | Arginase | |||
| A0A0A0LBW6 | Csa_3G199630 | EDA9 (AT4G34200) | 83% | 981 | 4 | 1,9E-02 | 33 | 7 | D-3-phosphoglycerate dehydrogenase | |||
| A0A0A0L0I0 | Csa_4G285780 | PA2 (AT5G06720) | 53% | 335 | 3,7 | 2,6E-02 | 33 | 3 | 1 | 3 | Peroxidase | |
| A0A0A0KA81 | Csa_6G088110 | AT2G20420 | 88% | 757 | 31 | 4 | 8 | 12 | Succinyl-CoA ligase | |||
| A0A0A0LBB3 | Csa_3G760530 | SVL1 (AT5G55480) | 56% | 851 | 6,6 | 2,3E-03 | 27 | Glycerophosphoryl diester- phosphodiesterase | ||||
| A0A0A0LFK3 | Csa_3G734240 | TIM9 (AT3G46560) | 82% | 162 | 26 | 0 | 2 | 1 | Translocase of the inner membrane 9 | |||
| A0A0A0KRD9 | Csa_5G613510 | UOX (AT2G26230) | 68% | 434 | 25 | Urate oxidase | ||||||
| A0A0A0L542_ A0A0A0LXV7 | Csa_3G078260 Csa_1G660150 | GPT2 (AT1G61800) | 75% | 568 | 5 | 8,4E-03 | 25 | Glucose-6-phosphate/phosphate translocator | ||||
| A0A0A0K1S9_ A0A0A0K3R7 | Csa_7G047450 Csa_7G047440 | AT2G20710 | 45% | 415 | 24 | 8 | 3 | 1 | PPR-type organelle RNA editing factor | |||
| A0A0A0LS81 | Csa_1G096620 | ASP1 (AT2G30970) | 88% | 768 | 22 | 1 | 11 | 0 | Aspartate transaminase | |||
| A0A0A0LQ27 | Csa_1G025890 | OAT (AT5G46180) | 79% | 738 | 21 | 7 | 3 | Ornithine delta aminotransferase | ||||
| A0A0A0L404 | Csa_4G646110 | FTSH4 (AT2G26140) | 81% | 1128 | 19 | 2 | 1 | 1 | ATP-dependent zinc metalloprotease | |||
| (B) | ||||||||||||
| A0A0A0KIM0 | Csa_6G497010 | NFS1 (AT5G65720) | 78% | 756 | 33 | 2 | Cysteine desulfurase | |||||
| A0A0A0KB82 | Csa_7G407690 | AT5G61310 | 67% | 95,1 | 4 | 27 | Cytochrome c oxidase subunit | |||||
| A0A0A0L3T5 | Csa_4G642530 | VDAC2 (AT5G67500) | 53% | 317 | 26 | Voltage-gated anion channel | ||||||
| A0A0A0KMP0 | Csa_5G321480 | AT2G07698 | 93% | 562 | 12 | 22 | 15 | 1 | ATP synthase subunit alpha | |||
| A0A0A0LGF5 | Csa_2G033990 | LON1 (AT5G26860) | 75% | 1456 | 10 | 22 | 9 | 3 | ATP-dependent serine protease | |||
| A0A0A0KW78 | Csa_4G017120 | TOM40-1 (AT3G20000) | 71% | 472 | 9 | 22 | 10 | 4 | Component of mitochondrial outer membrane translocase | |||
| A0A0A0LXK1 | Csa_1G629760 | SDH6 (AT1G08480) | 68% | 144 | 8 | 22 | 13 | 3 | Component of succinate dehydrogenase complex | |||
| A0A0A0KGU5 | Csa_6G500700 | MIC60 (AT4G39690) | 36% | 176 | 17 | 19 | 11 | 8 | Component of mitochondrial transmembrane lipoprotein complex | |||
| A0A0A0KGW6 | Csa_6G366300 | COS1 (AT2G44050) | 66% | 263 | 18,2 | 2,8E-06 | 16 | 5 | 6,7-Dimethyl-8-ribityllumazine synthase | |||
| A0A0A0KMM1 | Csa_5G047770 | AT1G14930 | 36% | 110 | 17 | 15 | Bet v1-type pathogenesis-related protein | |||||
| A0A0A0K9E8 | Csa_6G046410 | SD3 (AT4G00026) | 60% | 297 | 3 | 15 | 2 | 0 | Mitochondrial translocase | |||
| A0A0A0LSR2 | Csa_1G024260 | AT3G18240 | 62% | 506 | 14 | 13 | 9 | Mitochondrial ribosomal subunit | ||||
| (C) | ||||||||||||
| A0A0A0KKV4 | Csa_6G525450 | RFNR1 (AT4G05390) | 78% | 630 | 8 | 2 | 52 | Ferredoxin-NADP + reductase | ||||
| A0A0A0LDA3 | Csa_3G435020 | MPPa1 (AT1G51980) | 63% | 616 | 7,4 | 1,2E-03 | 13 | 6 | 49 | 12 | Subunit alpha of mitochondrial processing peptidase complex | |
| A0A0A0L7Y6 | Csa_3G164480 | AT4G15940 | 76% | 347 | 48 | Fumaryl acetoacetate hydrolase | ||||||
| A0A0A0KH76 | Csa_6G188090 | AT5G52370 | 57% | 151 | 44 | Mitochondrial 28S ribosomal protein S34 | ||||||
| E1B2J6 | GAPDH | GAPC1 | 88% | 610 | 9 | 35 | Glyceraldehyde 3 phosphate dehydrogenase | |||||
| A0A0A0KBL8 | Csa_6G077460 | TKL2 (AT2G45290) | 83% | 1306 | 6,8 | 1,9E-03 | 0 | 5 | 32 | 5 | Transketolase | |
| A0A0A0KRJ5 | Csa_5G168830 | MKP11 (AT5G17165) | 51% | 89 | 9,7 | 2,4E-04 | 29 | Late embryogenesis abundant protein | ||||
| A0A0A0M1R9_ A0A0A0LKR1 | Csa_1G574970 Csa_2G000830 | HXK1 (AT4G29130) | 74% | 757 | 11 | 4 | 27 | 3 | Hexokinase | |||
| A0A0A0KXY5 | Csa_4G337910 | AT5G63620 | 84% | 288 | 4 | 3 | 27 | 2 | Zinc-dependent alcohol dehydrogenase | |||
| A0A0A0LKD3 | Csa_2G346040 | UGP1 (AT5G17310) | 51% | 367 | 13 | 2 | 27 | 11 | UDP-glucose pyrophosphorylase | |||
| A0A0A0L2N5 | Csa_4G310720 | FAC1 (AT2G38280) | 80% | 1368 | 5,4 | 6,0E-03 | 22 | 11 | AMP deaminase | |||
| A0A0A0LZS4 | Csa_1G423090 | VDAC4 (AT5G57490) | 63% | 367 | 7 | 7 | 20 | 6 | Voltage-gated anion channel | |||
| A0A0A0LYA6 | Csa_1G532350 | AT4G33070 | 81% | 1042 | 3 | 6 | 19 | 5 | Thiamine pyrophosphate dependent pyruvate decarboxylase | |||
| A0A0A0LQ20 | Csa_2G403690 | CoxX3 (AT1G72020) | 66% | 138 | 16 | 12 | 17 | 9 | TonB-dependent heme receptor A | |||
| A0A0A0KGH2 | Csa_6G502730 | AT2G18330 | 75% | 891 | 17 | 2 | ATPase | |||||
| (D) | ||||||||||||
| A0A0A0LLE7_ A0A0A0KLP6 | Csa_2G372170 Csa_6G497310 | SHM1 (AT4G37930) | 80% | 869 | 9 | 2 | 10 | 28 | Serine hydroxymethyl transferase | |||
| A0A0A0KGA1 | Csa_6G135470 | ALDH5F1 (AT1G79440) | 77% | 813 | 3,5 | 3,0E-02 | 7 | 3 | 9 | 20 | Succinate-semialdehyde dehydrogenase | |
| A0A0A0L5J6 | Csa_3G115030 | AT5G40810 | 87% | 514 | 3,4 | 3,6E-02 | 6 | 8 | 5 | 18 | Cytochrome c1 component of cyt-bc1 complex | |
| A0A0A0LP60 | Csa_2G360050 | SDH5 (AT1G47420) | 56% | 266 | 4 | 4 | 4 | 16 | Succinate dehydrogenase subunit 5 | |||
| A0A0A0KP30 | Csa_5G199270 | PIP1;4 (AT4G00430) | 87% | 523 | 15,4 | 1,0E-05 | 10 | 11 | 3 | 19 | Aquaporin | |
| A0A0A0LJB4 | Csa_2G010420 | ALDH2B7 (AT1G23800) | 80% | 888 | 18,3 | 2,7E-06 | 0 | 7 | 3 | 21 | Aldehyde dehydrogenase | |
| A0A0A0KYN6 | Csa_4G192110 | GDH1 (AT5G18170) | 91% | 788 | 24,1 | 2,7E-07 | 9 | 11 | 2 | 20 | Glutamate dehydrogenase | |
| A0A0A0KWX8 | Csa_4G050830 | PGD1 (AT1G64190) | 87% | 892 | 15,9 | 8,2E-06 | 3 | 4 | 1 | 24 | Phosphogluconate dehydrogenase | |
| A0A0A0KX20 | Csa_4G052590 | NDPK4 (AT4G23900) | 78% | 387 | 4,8 | 9,4E-03 | 15 | 2 | 1 | 14 | Nucleoside diphosphate kinase | |
| A0A0A0LHY6 | Csa_3G836500 | FDH (AT5G14780) | 83% | 628 | 15,4 | 1,0E-05 | 2 | 2 | 1 | 22 | Formate dehydrogenase | |
| A0A0A0K9Z6 | Csa_6G004600 | CYSC1 (AT3G61440) | 79% | 588 | 28,4 | 6,5E-08 | 8 | 11 | 0 | 16 | b-cyanoalanine synthase/cysteine synthase | |
| A0A0A0KKD9 | Csa_5G149330 | BIP2 (AT5G42020) | 91% | 1229 | 3,3 | 3,7E-02 | 14 | 20 | Heat shock protein 70 | |||
| A0A0A0K7B3 | Csa_7G222870 | CYS4 (AT4G16500) | 35% | 96 | 10,2 | 1,9E-04 | 5 | 22 | Cysteine-type endopeptidase inhibitor | |||
| A0A0A0LYF4 | Csa_1G710160 | 33 | Cysteine-type endopeptidase inhibitor | |||||||||
| (D) | A0A0A0KVK8 A0A0A0LRR3_ A0A0A0LDZ4 | Csa_4G094520 Csa_2G369070 Csa_3G889810 | GF14 (AT1G35160) | 93% | 482 | 33 | 14-3-3 protein | |||||
| A0A0A0K6A8 | Csa_7G070770 | TUA4 (AT1G04820) | 98% | 869 | 3,5 | 3,3E-02 | 17 | Tubulin | ||||
Protein selection was based on the differential node Degree: Proteins with a Degree above the Network Average Degree (in bold) were retained. For each selected C. sativus protein, the C. sativus gene name, the name of A. thaliana homologous gene and the corresponding homology (in percent value and score), Linear Discriminant Analysis (LDA) parameters (only for differentially expressed proteins), and node Degree in the various nutritional conditions are reported. Homologies were retrieved by STRING database. Co-expression hubs in (A) Fe sufficiency (+Mo+Fe, −Mo+Fe), (B) Mo sufficiency (+Mo+Fe, +Mo−Fe), (C) Fe starvation (+Mo−Fe, −Mo−Fe) and (D) Mo starvation (−Mo+Fe, −Mo−Fe) are shown. Each accession number within brackets refers to the A. thaliana gene reported on the upper line.