Table 4.

Differentially abundant transcripts both at proteomic and transcriptomic levels in M12 under waterlogging.

Protein Accession	Protein Description	MW (kDa)	M12W/M12CK Ratio	M12W/M12CK p-Value	Protein LOG2 M12W/M12CK	Regulation	Transcription Log2 M12_W/M12_CK	p adj	Regulation	Type
Cluster-1252.18690_orf1	Unknown	42.266	1.816	5.1953 × 10−3	0.860764203	Up	1.7749	9.0263 × 10−7	Up	Up-Up
Cluster-1252.20320_orf1	Probable mannitol dehydrogenase OS = Medicago sativa GN=CAD1 PE=1 SV=1	39.526	1.414	2.8745 × 10−2	0.49978212	Up	1.664	2.132 × 10−4	Up	Up-Up
Cluster-1252.24948_orf1	Acidic endochitinase OS=Cicer arietinum PE=2 SV=1	33.034	2.91	5.1816 × 10−3	1.541019153	Up	3.0386	4.4982 × 10−18	Up	Up-Up
Cluster-1252.25469_orf1	Probable glutathione S-transferase OS=Glycine max GN=HSP26-A PE=2 SV=1	26.335	2.141	1.02394 × 10−3	1.098284796	Up	2.0505	8.3503 × 10−25	Up	Up-Up
Cluster-1252.29574_orf1	Unknown	56.855	1.302	1.41228 × 10−2	0.380729449	Up	1.0417	3.2239 × 10−4	Up	Up-Up
Cluster-1252.33343_orf1	“Ornithine aminotransferase, mitochondrial OS=Arabidopsis thaliana GN=DELTA-OAT PE=1 SV=1”	51.439	1.503	4.2365 × 10−8	0.587845009	Up	1.4006	2.5266 × 10−19	Up	Up-Up
Cluster-1252.35376_orf1	Unknown	22.309	3.216	3.69926 × 10−13	1.685267407	Up	2.8743	1.7054 × 10−62	Up	Up-Up
Cluster-1252.36163_orf1	Expansin-like B1 OS=Arabidopsis thaliana GN=EXLB1 PE=2 SV=2	30.779	2.387	1.83814 × 10−2	1.255198566	Up	1.3227	1.0834 × 10−4	Up	Up-Up
Cluster-1252.38004_orf2	Protein C2-DOMAIN ABA-RELATED 9 OS=Arabidopsis thaliana GN=CAR9 PE=2 SV=1	21.642	1.534	7.6395 × 10−5	0.617298483	Up	1.4498	1.0054 × 10−10	Up	Up-Up
Cluster-1252.39652_orf1	18 kDa seed maturation protein OS=Glycine max GN=GMPM1 PE=2 SV=1	12.611	1.805	1.62154 × 10−3	0.851998837	Up	2.2232	4.4188 × 10−12	Up	Up-Up
Cluster-1252.41663_orf1	Stress-related protein OS=Phaseolus vulgaris GN=SRP PE=2 SV=1	146.66	1.7	3.5979 × 10−5	0.765534746	Up	1.1772	1.5419 × 10−12	Up	Up-Up
Cluster-1252.41945_orf1	Glucose-1-phosphate adenylyltransferase large subunit 1 (Fragment) OS=Solanum tuberosum GN=AGPS1 PE=2 SV=1	59.046	2.277	4.6658 × 10−2	1.187134291	Up	2.2953	1.4116 × 10−4	Up	Up-Up
Cluster-1252.42642_orf1	Unknown	16.163	3.21	9.99201 × 10−16	1.682573297	Up	1.6109	5.0453 × 10−27	Up	Up-Up
Cluster-1252.42960_orf1	Early nodulin-like protein 2 OS=Arabidopsis thaliana GN=At4g27520 PE=1 SV=1	103.53	1.698	1.90671 × 10−5	0.763836459	Up	1.0147	2.9677 × 10−13	Up	Up-Up
Cluster-1252.42962_orf1	Aldo-keto reductase family 4 member C9 OS=Arabidopsis thaliana GN=AKR4C9 PE=1 SV=1	36.025	1.447	5.56521 × 10−12	0.533064922	Up	1.5685	3.609 × 10−25	Up	Up-Up
Cluster-1252.43381_orf1	Thaumatin-like protein OS=Oryza sativa subsp. japonica GN=Os12g0628600 PE=1 SV=1	20.658	4.005	2.2805 × 10−3	2.001802243	Up	1.923	5.4445 × 10−14	Up	Up-Up
Cluster-1252.43664_orf1	Cinnamoyl-CoA reductase 1 OS=Arabidopsis thaliana GN=CCR1 PE=1 SV=1	34.902	2.775	1.0 × 10−32	1.472487771	Up	1.4878	7.6623 × 10−82	Up	Up-Up
Cluster-1252.43700_orf1	Vacuolar-processing enzyme OS=Vicia sativa PE=1 SV=1	148.25	1.998	2.2366 × 10−3	0.998556583	Up	1.237	4.6915 × 10−108	Up	Up-Up
Cluster-1252.44442_orf1	“Superoxide dismutase [Fe] 2, chloroplastic OS=Arabidopsis thaliana GN=FSD2 PE=1 SV=1”	36.823	1.725	3.0282 × 10−10	0.786596362	Up	1.0925	1.076 × 10−3	Up	Up-Up
Cluster-1252.45489_orf1	Unknown	87.568	1.436	2.8214 × 10−4	0.522055749	Up	1.1902	4.0089 × 10−11	Up	Up-Up
Cluster-1252.45907_orf1	Methylecgonone reductase OS=Erythroxylum coca PE=1 SV=1	35.219	1.928	1.2051 × 10−7	0.947105052	Up	1.071	1.6158 × 10−5	Up	Up-Up
Cluster-1252.48706_orf1	Delta-1-pyrroline-5-carboxylate synthase OS=Oryza sativa subsp. japonica GN=P5CS PE=2 SV=2	82.353	2.766	4.1957 × 10−8	1.467801156	Up	4.8411	2.0236 × 10−298	Up	Up-Up
Cluster-1252.50314_orf1	1-aminocyclopropane-1-carboxylate oxidase homolog 5 OS=Arabidopsis thaliana GN=2A6 PE=2 SV=2	47.587	2.108	7.0431 × 10−11	1.075874867	Up	2.6988	1.3474 × 10−28	Up	Up-Up
Cluster-1252.53143_orf1	“1,4-alpha-glucan-branching enzyme 1, chloroplastic/amyloplastic (Fragment) OS=Pisum sativum GN=SBEII PE=1 SV=1”	98.938	2.033	2.9402 × 10−7	1.023610215	Up	1.8785	8.7896 × 10−8	Up	Up-Up
Cluster-1252.59078_orf1	Pathogenesis-related protein PR-4B OS=Nicotiana tabacum PE=2 SV=1	19.406	2.258	3.0823 × 10−2	1.175045486	Up	2.4968	4.4984 × 10−5	Up	Up-Up
Cluster-1252.62468_orf1	Unknown	107.76	8.756	6.3273 × 10−5	3.130271955	Up	3.225	2.9758 × 10−39	Up	Up-Up
Cluster-1252.65950_orf1	Galactinol--sucrose galactosyltransferase OS=Pisum sativum GN=RFS PE=1 SV=1	90.573	1.834	6.6447 × 10−10	0.874993639	Up	2.8804	2.2919 × 10−15	Up	Up-Up
Cluster-1252.35865_orf1	Tubulin alpha chain OS=Prunus dulcis GN=TUBA PE=2 SV=1	54.36	0.648	2.3014 × 10−3	−0.625934282	Down	−1.5125	1.0164 × 10−18	Down	Down-Down
Cluster-1252.40636_orf1	1-aminocyclopropane-1-carboxylate oxidase OS=Prunus mume GN=ACO1 PE=2 SV=1	39.544	0.435	4.7576 × 10−6	−1.200912694	Down	−1.535	1.4095 × 10−47	Down	Down-Down
Cluster-1252.43303_orf1	“Ferredoxin--nitrite reductase, chloroplastic OS=Betula pendula GN=NIR1 PE=2 SV=1”	69.24	0.423	1.0 × 10−32	−1.241270432	Down	−2.8277	4.993 × 10−52	Down	Down-Down
Cluster-1252.43480_orf1	“Protochlorophyllide reductase, chloroplastic OS=Pisum sativum GN=3PCR PE=1 SV=1”	43.178	0.645	1.4187 × 10−11	−0.632628934	Down	−1.0364	1.1526 × 10−50	Down	Down-Down
Cluster-1252.43550_orf1	β-galactosidase 1 OS=Arabidopsis thaliana GN=BGAL1 PE=2 SV=1	93.798	0.506	2.2202 × 10−5	−0.98279071	Down	−1.5947	5.4211 × 10−54	Down	Down-Down
Cluster-1252.44318_orf1	Nitrate reductase [NADH] OS=Lotus japonicus GN=NIA PE=3 SV=1	102.62	0.623	1.33524 × 10−3	−0.682695932	Down	−2.0582	3.1915 × 10−25	Down	Down-Down
Cluster-1252.45309_orf1	Universal stress protein A-like protein OS=Arabidopsis thaliana GN=At3g01520 PE=1 SV=2	18.198	0.552	2.9101 × 10−2	−0.857259828	Down	−1.2288	1.3773 × 10−29	Down	Down-Down
Cluster-1252.48945_orf1	Unknown	40.668	0.512	2.36871 × 10−11	−0.965784285	Down	−2.4873	1.4274 × 10−10	Down	Down-Down