Table 1. Gene-gene edges modified by a discrete variable in the D2 consensus network with high frequencies (f > 0.85).
| f | r | Node 1 | Description | Node 2 | Description |
|---|---|---|---|---|---|
| If DCE (and all higher chlorinated ethenes, when provided) was available to be and was respired (1) or not (0) | |||||
| 0.85 | 0.73 | DET0006 | histidyl-tRNA synthetase | DET1386 | hypothetical protein |
| 0.91 | 0.78 | - | EA feed rate over the final 48 hrs | - | respiration rate of DCE |
| 0.88 | -0.23 | - | respiration rate of PCE | DET0315 | sensory box sensor histidine kinase |
| 0.89 | 0.92 | DET0564 | ATP synthase subunit B | DET1263 | DAK2 domain protein |
| 0.89 | 0.92 | DET1225 | hypothetical protein | DET1417 | formyltransferase |
| If TCE (and PCE, when provided) was available to be and was respired (1) or not (0) | |||||
| 0.96 | 0.88 | DET1477 | hypothetical protein | DET1554 | hypothetical protein |
| 0.90 | 0.95 | DET1510 | hypothetical protein | DET0657 | phosphoribosyltransferase |
| If PCE was available to be and was respired (1) or not (0) | |||||
| 0.98 | 0.19 | tRNA | Cys-1 | tRNA | Gly-3 |
| 0.86 | 0.66 | DET0414 | hypothetical protein | DET0165 | ISDet2, transposase orfA |
| 0.90 | 0.93 | DET1041 | PQQ enzyme repeat domain protein | DET1039 | SpoIIIJ-associated protein Jag |
| If DCE was detected above background levels (1) or not (0) | |||||
| 0.94 | 0.32 | DET0057 | ATP-dependent Clp protease, ClpC | - | concentration of DCE |
| 0.94 | -0.72 | DET0128 | cobyrinic acid a,c-diamide synthase | DET0299 | transcriptional regulator, Crp/Fnr family |
| 0.85 | 0.81 | DET0840 | adenylosuccinate lyase | DET0439 | FtsK/SpoIIIE family protein |
| 0.87 | -0.68 | DET1430 | HypA hydrogenase nickel insertion protein | - | methanogenesis rate |
| 0.79 | 0.88 | DET1431 | HypB hydrogenase accessory protein | DET1433 | hydrogenase assembly chaperone |
| 0.94 | 0.74 | DET1476 | DNA binding domain, excisionase family | DET0981 | tRNA pseudouridine synthase B |
| If PCE was detected above background levels (1) or not (0) | |||||
| 0.88 | 0.84 | DET1345 | tagatose 1,6-diphosphate aldolase | DET1530 | sensor histidine kinase |
| If an electron donor was being provided to the culture (1) or not (0) | |||||
| 0.93 | 0.74 | DET1084 | DNA packaging protein, putative | DET1070 | endolysin, putative |
| 0.88 | 0.82 | DET1244 | NADPH-dependent FMN reductase | DET1005 | transcriptional regulator, ArsR family |
| 0.90 | 0.78 | DET1570 | hydrogenase, group 4, HycG subunit | DET1106 | hypothetical protein |
| If the culture displayed inhibited growth (1) or not (0) | |||||
| 0.86 | 0.90 | DET0111 | [Ni/Fe] hydrogenase, small subunit | DET0112 | [Ni/Fe] hydrogenase, Fe-S cluster |
| 0.86 | 0.74 | DET0451 | malate dehydrogenase, NAD-dependent | DET0115 | ABC transporter, permease protein |
| 0.92 | 0.81 | DET0610 | hypothetical protein | tRNA | Cys-1 |
| 0.99 | 0.76 | DET1111 | ATP-binding protein | DET0097 | iron dependent repressor, putative |
| If the culture displayed inhibited growth because of DCE (1) or not (0) | |||||
| 0.96 | 0.92 | tRNA | Val-2 | tRNA | Ser-1 |
| 0.99 | 0.88 | DET0343 | cell division protein FtsZ | DET0342 | cell division protein FtsA |
| 0.94 | 0.70 | DET0383 | hypothetical protein | DET1438 | hypothetical protein |
| 0.95 | 0.90 | DET0591 | hypothetical protein | DET0334 | polyA polymerase family protein |
| 0.85 | 0.77 | DET0839 | phosphoribosylaminoimidazole carboxylase | DET0607 | hypothetical protein |
| 0.87 | 0.85 | DET0920 | iron-sulfur cluster-binding protein | DET0921 | hypothetical protein |
| 0.92 | 0.86 | DET1207 | protein export protein, putative | DET0543 | fatty acid/phospholipid synthesis |
| 0.96 | 0.80 | DET1350 | DNA-binding response regulator | DET0922 | twitching mobility protein |
| 0.89 | 0.32 | DET1446 | excisionase family DNA binding protein | DET0432 | DNA-binding response regulation |
The relationship identified occurs when the discrete variable is set to 1. Gray squares indicate non-gene variables related to experimental conditions. The correlation score (r value) between the intensity values of two probes across all datasets is presented to display whether the relationship between the intensity values of the probes is positive or negative.