Table IV. Identification of candidate genes based on their connection with known symbiosis genes in the 227 subnetwork.
| Gene | Gene Description | Connectivity Scorea |
|---|---|---|
| Medtr3g072710 | Nodulation-signaling pathway2 protein (NSP2) | 0.153 |
| Medtr5g086110 | LysM domain-containing receptor-like kinase | 0.122 |
| Medtr1g056530 | Nuclear transcription factor Y subunit A-10 (NF-YA1) | 0.083 |
| Medtr5g086130 | LysM receptor kinase (LYK3) | 0.076 |
| Medtr7g082260 | Zinc finger protein | 0.075 |
| contig_119095_1 | SUPERMAN-like zinc finger protein | 0.072 |
| Medtr3g031270 | Wound-induced protein | 0.071 |
| Medtr5g099060 | Nodule inception protein (NIN) | 0.070 |
| Medtr5g086120 | Receptor-like protein kinase (LYK4) | 0.069 |
| Medtr7g085810 | ET-responsive TF (ERN1) | 0.069 |
| contig_56789_1 | Calmodulin-binding protein | 0.067 |
| Medtr4g079760 | TF basic helix-loop-helix30 | 0.064 |
| Medtr3g015490 | Two-component response regulator ARR9 | 0.064 |
| Medtr2g101830 | Rop guanine nucleotide-exchange factor (RopGEF12) | 0.064 |
| contig_103831_1 | Myb-like transcription factor Myb | 0.062 |
| contig_60935_1 | Protein phosphatase2C | 0.056 |
| Medtr7g011900 | Isoliquiritigenin 2′-O-methyltransferase | 0.056 |
| Medtr5g025840 | Kinase-like protein | 0.053 |
| contig_8047_1 | LOB domain protein-like protein (LBD16) | 0.052 |
| Medtr4g127140 | MADS box transcription factor | 0.050 |
| Medtr5g025850 | Receptor-like protein kinase | 0.048 |
| contig_49939_2 | Receptor-like kinase | 0.044 |
| AC235664_10 | 4-Hydroxy-3-methyl-but-2-enyl diphosphate reductase (HDR) | 0.044 |
| contig_167979_1 | Chaperone protein DnaJ-like protein | 0.044 |
| contig_245351_1 | Receptor protein kinase | 0.044 |
| contig_76132_1 | HDR | 0.044 |
| Medtr4g104060 | Unknown protein | 0.044 |
| Medtr5g010010 | 2-C-Methyl-d-erythritol 2 4-cyclodiphosphate synthase (MCS) | 0.044 |
| Medtr6g082180 | Unknown protein | 0.044 |
| Medtr7g104250 | Unknown protein | 0.044 |
| Medtr5g019070 | LRR receptor-like Ser/Thr-protein kinase FEI | 0.043 |
| Medtr3g086320 | Pectate lyase | 0.043 |
| Medtr2g068960 | ACC oxidase homologb | 0.040 |
| Medtr2g069020 | ACC oxidase homologb | 0.040 |
| Medtr8g097190 | Unknown protein | 0.040 |
| contig_30837_1 | Receptor-like kinase | 0.040 |
| Medtr2g068650 | Kinase-like protein | 0.039 |
| Medtr4g051330 | Two-component response regulator ARR9 | 0.039 |
| CX549419 | Weakly similar to UniRef100 A7P585 (Vitis vinifera) | 0.039 |
| contig_60385_1 | Basic helix-loop-helix TF-like protein | 0.039 |
| Medtr1g031540 | Receptor Ser/Thr kinase | 0.039 |
| contig_68802_2 | Cytochrome P450 | 0.038 |
| Medtr4g107970 | WRKY transcription factor | 0.038 |
| Medtr5g033030 | Multidrug resistance protein ATP-binding cassette transporter family | 0.038 |
| Medtr2g069250 | Nodule-specific Gly-rich protein3C | 0.038 |
| Medtr2g019750 | ET-responsive transcription factor3b | 0.038 |
| Medtr8g026680 | Rac GTPase-activating protein | 0.038 |
| contig_55524_1 | Zinc finger protein | 0.037 |
| AC233082_23 | Receptor-like kinase | 0.037 |
| Medtr5g026760 | Kinase-like protein | 0.036 |
| Medtr8g074530 | Unknown protein | 0.033 |
| Medtr7g020980 | ET-responsive TF (ERF115) | 0.033 |
| contig_62786_1 | Inositol-tetrakisphosphate 1-kinase | 0.032 |
| Medtr3g008760 | 21-kD protein | 0.032 |
| Medtr6g052300 | Metal transporter cyclin and CBS domain divalent metal cation transport mediator2 | 0.032 |
| contig_94824_1 | LRR-RLK protein | 0.032 |
a
The connectivity score, obtained by applying a regularized Laplacian kernel method to the inferred regulatory network, measures connectivity to the known symbiosis genes. The top 56 genes shown were selected such that their score was 2 sd above the mean. Input symbiosis genes are shown in boldface.
b
Annotated as 2-oxoglutarate-Fe(II) oxygenase family oxidoreductase in IMGA 4.0 version 1.