Table 3.

List of genes downregulated by ≥1.5-fold (p < 0.05) in rat middle ear mucosae colonized by MRSA and PA and either downregulated or upregulated with MRSA or PA single species colonization.

Serial number	Gene accession	Gene ID	Gene name	Protein	Fold change in mixed inoculation	p-value	Fold change with single species SA	p-value	Fold change with single species PA	p-value
1	XLOC_000033	TBIG000033	TXLNB	Beta-taxilin	−7.41	0.04245	−1.39	0.01125	−7.68	0.07995
2	XLOC_005477	TBIG005477	SCN4A	Sodium channel protein type 4 subunit alpha	−5.49	0.02615	−1.34	0.074	−4.26	0.11755
3	XLOC_021210	TBIG021210	GAG	Gag polyprotein	−5.22	0.044	0.78	0.2248	−0.722	0.4373
4	XLOC_027720	TBIG027720	IGSF1	Immunoglobulin superfamily member 1	−4.53	0.0182	−1.13	0.19385	−5.06	0.14935
5	XLOC_013130	TBIG013130	LDLRAD1	Low-density lipoprotein receptor class A domain-containing protein 1	−4.36	0.0083	−1.15	0.2058	−1.93	0.15705
6	XLOC_027382	TBIG027382	POL	Retrovirus-related Pol polyprotein LINE-1	−4.29	0.0183	−1.76	0.07165	−4.89	0.095
7	XLOC_012347	TBIG012347	GAG-POL	Gag-Pol polyprotein	−4.25	0.00015	0.841	0.0705	−0.867	0.15245
8	XLOC_015004	TBIG015004	TNXB	Tenascin-X	−4.14	0.0376	−2.21	0.25835	−3	0.0938
9	XLOC_024947	TBIG024947	GRIA4	Glutamate receptor 4	−4.06	0.04955	−1.7	0.0813	−2.26	0.1075
10	XLOC_014321	TBIG014321	TTC24	Tetratricopeptide repeat protein 24	−4.04	0.0285	−0.657	0.4197	−1.2	0.28155
11	XLOC_026757	TBIG026757	POL	Pol polyprotein	−4.03	0.02135	0.779	0.21675	1.18	0.15825
12	XLOC_020111	TBIG020111	NT5C1A	Cytosolic 5'-nucleotidase 1A	−3.93	0.00125	−1.39	0.0508	−2.43	0.0548
13	XLOC_002039	TBIG002039	MARK4	MAP/microtubule affinity-regulating kinase 4	−3.65	0.0475	−1.43	0.4849	−3.48	0.0536
14	XLOC_007497	TBIG007497	BRINP3	BMP/retinoic acid-inducible neural-specific protein 3	−3.63	0.0429	−1.46	0.1324	−3.66	0.13615
15	XLOC_024201	TBIG024201	POL	Pol polyprotein	−3.57	0.0373	−0.937	0.2889	−1.6	0.2579
16	XLOC_006129	TBIG006129	POL	Pol polyprotein	−3.38	0.04745	−1.18	0.207	−1.52	0.34225
17	XLOC_005475	TBIG005475	GH1	Somatotropin	−3.34	0.04165	0.851	0.2985	−0.925	0.49845
18	XLOC_024602	TBIG024602	HCN4	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4	−3.27	0.03825	−0.742	0.37845	−1.53	0.27585
19	XLOC_021698	TBIG021698	RGS6	Regulator of G-protein signaling 6	−3.25	0.02615	−1.38	0.14185	−1.96	0.20475
20	XLOC_006065	TBIG006065	OSTN	Osteocrin	−3.23	0.04325	−1.79	0.04165	−2.8	0.081
21	XLOC_021434	TBIG021434	ALK	ALK tyrosine kinase receptor	−3.18	0.0397	−1.86	0.0675	−3.07	0.08475
22	XLOC_026950	TBIG026950	EGFL6	Epidermal growth factor-like protein 6	−3.13	0.0404	−0.986	0.2498	−1.45	0.2599
23	XLOC_021001	TBIG021001	NCMAP	Noncompact myelin-associated protein	−3.13	0.0497	−1.11	0.50945	−1.23	0.5089
24	XLOC_004000	TBIG004000	GRIA1	Glutamate receptor 1	−3.05	0.0488	−2.95	0.0636	−2.59	0.0773
25	XLOC_021987	TBIG021987	KCNK3	Potassium channel subfamily K member 3	−2.98	0.03695	−2.13	0.0539	−2.07	0.1183
26	XLOC_008308	TBIG008308	NAA11	N-alpha-acetyltransferase 11	−2.97	0.02785	−1.27	0.1347	−1.53	0.1725
27	XLOC_003922	TBIG003922	TRIM7	Tripartite motif-containing protein 7	−2.93	0.0133	−1.02	0.11075	−1.47	0.10675
28	XLOC_010040	TBIG010040	POL	Pol polyprotein	−2.86	0.01455	−1.46	0.06215	−2.43	0.0726
29	XLOC_017690	TBIG017690	BCAS1	Breast carcinoma-amplified sequence 1 homolog	−2.65	0.04765	−1.54	0.07675	−0.974	0.3948
30	XLOC_002797	TBIG002797	SNRPN	Small nuclear ribonucleoprotein-associated protein N	−2.65	0.0201	−1.4	0.06855	−2.02	0.06625
31	XLOC_023030	TBIG023030	COL14A1	Collagen alpha-1(XIV) chain	−2.62	0.0069	−0.904	0.16355	−1.16	0.15975
32	XLOC_023753	TBIG023753	KLHL38	Kelch-like protein 38	−2.62	0.0302	−0.989	0.17215	−2.69	0.0851
33	XLOC_002608	TBIG002608	HBB2_RAT	Hemoglobin subunit beta-2	−2.55	0.0001	−2.36	5.00E−05	−3.34	5.00E−05
34	XLOC_024012	TBIG024012	COL2A1	Collagen alpha-1(II) chain	−2.51	0.00715	−0.616	0.24645	1.09	0.10775
35	XLOC_007817	TBIG007817	NFASC	Neurofascin	−2.46	0.02025	−1.47	0.09665	−2.29	0.08025
37	XLOC_018133	TBIG018133	MEST	Mesoderm-specific transcript homolog protein	−2.43	0.03235	−1.11	0.1112	−1.91	0.07395
38	XLOC_022758	TBIG022758	LINGO3	Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 3	−2.35	0.0387	−1.42	0.0885	−1.4	0.18525
39	XLOC_005055	TBIG005055	CHRNB1	Acetylcholine receptor subunit beta	−2.25	0.0174	−1.12	0.10445	−1.7	0.08505
40	XLOC_009184	TBIG009184	CDHR3	Cadherin-related family member 3	−2.25	0.04445	−0.978	0.13985	−1.47	0.15415
41	XLOC_014711	TBIG014711	CAPSL	Calcyphosin-like protein	−2.24	0.04895	−0.886	0.25825	−0.976	0.37135
42	XLOC_003432	TBIG003432	POL	Pol polyprotein	−2.11	0.0243	−1.35	0.0438	−1.65	0.07025
43	XLOC_022093	TBIG022093	EGLN3	Egl nine homolog 3	−2.09	0.02785	−0.962	0.11	−0.67	0.37785
44	XLOC_017633	TBIG017633	MATN4	Matrilin-4 [Source:SWISS;Acc:O89029]	−2.02	0.0068	−0.87	0.0838	−0.925	0.15585
45	XLOC_017934	TBIG017934	GAG-POL	Gag-Pol polyprotein	−1.92	0.0217	−0.381	0.4882	−0.885	0.2449
46	XLOC_000295	TBIG000295	SSC5D	Soluble scavenger receptor cysteine-rich domain-containing protein SSC5D	−1.91	0.00235	−0.86	0.062	−1.13	0.05595
47	XLOC_020236	TBIG020236	TCEA3	Transcription elongation factor A protein 3	−1.8	0.04715	−0.75	0.2413	−1.45	0.1176
48	XLOC_019566	TBIG019566	POL	Pol polyprotein	−1.75	0.00645	−0.592	0.29525	−1.36	0.0589
49	XLOC_024924	TBIG024924	FAM198A	Protein FAM198A	−1.68	0.04485	−0.975	0.104	−1.57	0.0906
50	XLOC_016802	TBIG016802	-	-	−1.68	0.01715	−0.262	0.6802	−1.08	0.13725
51	XLOC_010859	TBIG010859	AGTPBP1	Cytosolic carboxypeptidase 1	−1.67	0.01575	−0.817	0.1006	−1.66	0.0367
52	XLOC_002382	TBIG002382	ST8SIA2	Alpha-2,8-sialyltransferase 8B	−1.67	0.04965	−0.846	0.171	−1.09	0.23515
53	XLOC_026579	TBIG026579	CCDC108	Coiled-coil domain-containing protein 108	−1.66	0.01635	−0.31	0.5204	−0.735	0.2972
54	XLOC_027640	TBIG027640	CHRDL1	Chordin-like protein 1	−1.62	0.00485	−0.842	0.0639	−1.81	0.0037
55	XLOC_002898	TBIG002898	ADAM8	Disintegrin and metalloproteinase domain-containing protein 8	−1.59	0.00935	−0.908	0.0545	−0.97	0.12135
56	XLOC_021028	TBIG021028	UBXN10	UBX domain-containing protein 10	−1.58	0.01805	−0.353	0.5061	−1.22	0.08675
57	XLOC_013884	TBIG013884	C1ORF173	Uncharacterized protein C1orf173	−1.56	0.019	−0.068	0.88615	−0.855	0.18325
58	XLOC_024898	TBIG024898	DLEC1	Deleted in lung and esophageal cancer protein 1	−1.56	0.03495	−0.467	0.3517	−1.07	0.14125
59	XLOC_001829	TBIG001829	SLC22A3	Solute carrier family 22 member 3	inf	5.00E−05	−1.36	0.2606	−3.68	0.19145
60	XLOC_003476	TBIG003476	POL	Pol polyprotein	inf	5.00E05	−0.582	0.23855	−10.4	0.2431
61	XLOC_004811	TBIG004811	RPS2	40S ribosomal protein S2	inf	5.00E−05	0.17	0.71865	inf	5.00E−05
62	XLOC_006114	TBIG006114	RPL9	60S ribosomal protein L9	inf	5.00E−05	−0.538	0.5414	inf	5.00E−05
63	XLOC_006289	TBIG006289	MYH15	Myosin-15	inf	5.00E−05	−1.09	0.28855	−6.22	0.2431
64	XLOC_006508	TBIG006508	GAG	Gag polyprotein	inf	5.00E−05	−0.187	0.8494	−3.29	0.21805
65	XLOC_009108	TBIG009108	GAG-POL	Gag-Pol polyprotein	inf	5.00E−05	−0.5	0.5663	−6.64	0.24325
66	XLOC_013224	TBIG013224	RPS2	40S ribosomal protein S2	inf	5.00E−05	0.11	0.8856	−7.12	0.24315
67	XLOC_017320	TBIG017320	ACTC1	Actin, alpha cardiac muscle 1	inf	5.00E−05	−0.929	0.0515	−11.1	0.2431
68	XLOC_022977	TBIG022977	STAC3	SH3 and cysteine-rich domain-containing protein 3	inf	5.00E−05	−1.31	0.0224	−8.87	0.1708
69	XLOC_023915	TBIG023915	CYP2D1	Cytochrome P450 2D1	inf	5.00E−05	1.29	0.09275	−4.64	0.16405
70	XLOC_026493	TBIG026493	MSTN	Growth/differentiation factor 8	inf	5.00E−05	−2.2	0.1506	−5.46	0.2456
71	XLOC_027253	TBIG027253	CX064_MOUSE	Uncharacterized protein CXorf64 homolog	inf	5.00E−05	−1.48	0.1895	−5.75	0.2454
72	XLOC_022618	TBIG022618	ENV	Envelope glycoprotein	inf	0.0004	−0.993	0.41135	inf	0.0008
73	XLOC_005431	TBIG005431	NEDD4	E3 ubiquitin-protein ligase NEDD4	inf	0.00345	−1.81	0.2551	−4.4	0.25485
74	XLOC_016973	TBIG016973	NEB	Nebulin	inf	0.00495	−0.73	0.57485	−2.83	0.2479
75	XLOC_019744	TBIG019744	CALB1	Calbindin	inf	0.0053	−1.73	0.2773	−3.48	0.2558
76	XLOC_020636	TBIG020636	15.5 KDA FABP	Major urinary protein	inf	0.0053	−3.54	0.1979	−2.95	0.2434
77	XLOC_022462	TBIG022462	HV208_HUMAN	Ig heavy chain V-II region SESS	inf	0.0053	−0.717	0.578	−4.71	0.2508
78	XLOC_027795	TBIG027795	POL	Pol polyprotein	inf	0.0053	−3	0.1555	−3.64	0.25175
79	XLOC_007006	TBIG007006	KIF19	Kinesin-like protein KIF19	inf	0.0058	−1.9	0.2472	−4.39	0.2531
80	XLOC_017904	TBIG017904	POL	Retrovirus-related Pol polyprotein LINE-1	inf	0.00575	−3.28	0.2009	−1.76	0.3774
81	XLOC_019217	TBIG019217	OXTR	Oxytocin receptor	inf	0.0058	−2.29	0.19495	−4.46	0.2524
82	XLOC_007150	TBIG007150	DNAH10	Dynein heavy chain 10, axonemal	inf	0.01035	−3.34	0.26695	−2.62	0.2963
83	XLOC_016972	TBIG016972	NEB	Nebulin	inf	0.0097	−2.55	0.23375	−3.61	0.2679
84	XLOC_009140	TBIG009140	DUSP13	Dual specificity protein phosphatase 13 isoform A	inf	0.0117	−0.865	0.6321	−3.34	0.27455
85	XLOC_006921	TBIG006921	CD209L2	CD209 antigen-like protein 2	inf	0.01335	−0.951	0.6269	−3.07	0.2863
86	XLOC_009994	TBIG009994	GAG	Gag polyprotein	inf	0.01335	1.01	0.46895	0.352	0.8164
87	XLOC_009143	TBIG009143	DUSP13	Dual specificity protein phosphatase 13 isoform A	inf	0.0252	−0.929	0.6643	−2.67	0.42285
88	XLOC_007324	TBIG007324	POL	Pol polyprotein	inf	0.0387	0.404	0.83325	0.731	0.77005