9  Oxidative Stress Panel

❖ Data

❖ Description

Variable	Description
Experiment	ID of the experimental batch (different plates)
Mouse	Mouse unique identifier
Stage	Developmental stage
Pathway	Biological pathway the Gene is involved in
Condition	Hypoxia condition: Normoxia (N) vs Intermittent Hypoxia (IH)
DCq	Delta Cq
Fold	Fold change

Variable	Description
Experiment	ID of the experimental batch (different plates)
Mouse	Mouse unique identifier
Stage	Developmental stage
Pathway	Biological pathway the Gene is involved in
Condition	Hypoxia condition: Normoxia (N) vs Intermittent Hypoxia (IH)
DCq	Delta Cq
Fold	Fold change

9.1 Data Exploration

Split by Pathway:

Antioxidant Response

Gene	Condition	Mean	SD	Variance	CoV	IQR	Min	Max	Skewness	Kurtosis	n
Cat	N	5.004	0.149	0.022	0.03	0.265	4.751	5.212	−0.148	−1.354	15
Cat	IH	5.114	0.092	0.008	0.018	0.187	4.965	5.22	−0.338	−1.354	10
Gpx1	N	4.231	0.167	0.028	0.04	0.159	3.98	4.586	0.88	0.871	15
Gpx1	IH	4.334	0.074	0.005	0.017	0.132	4.222	4.443	0.3	−0.807	10
Gpx3	N	6.32	0.251	0.063	0.04	0.304	6.01	6.796	0.788	−0.375	15
Gpx3	IH	6.303	0.15	0.022	0.024	0.307	6.099	6.498	0.118	−1.717	10
Gpx4	N	4.28	0.116	0.013	0.027	0.22	4.135	4.52	0.505	−0.436	15
Gpx4	IH	4.394	0.149	0.022	0.034	0.266	4.145	4.601	−0.296	−0.941	10
Gpx7	N	7.08	0.156	0.024	0.022	0.262	6.826	7.312	−0.274	−1.088	15
Gpx7	IH	7.319	0.203	0.041	0.028	0.355	7.09	7.681	0.452	−1.092	10
Gpx8	N	7.162	0.152	0.023	0.021	0.243	6.807	7.347	−0.691	0.312	15
Gpx8	IH	7.298	0.222	0.049	0.03	0.489	7.053	7.605	0.329	−1.575	10
Gsr	N	4.903	0.221	0.049	0.045	0.262	4.55	5.413	0.459	1.017	15
Gsr	IH	5.029	0.17	0.029	0.034	0.273	4.755	5.299	−0.3	−0.573	10
Gss	N	7.832	0.108	0.012	0.014	0.158	7.581	8.019	−0.757	0.953	15
Gss	IH	7.785	0.291	0.084	0.037	0.592	7.383	8.193	−0.154	−1.518	10
Gstk1	N	7.971	0.125	0.016	0.016	0.176	7.677	8.156	−0.676	0.787	15
Gstk1	IH	8.084	0.108	0.012	0.013	0.152	7.863	8.239	−0.778	0.746	10
Gstm1	N	4.838	0.133	0.018	0.028	0.166	4.51	4.985	−1.145	1.273	15
Gstm1	IH	4.518	0.127	0.016	0.028	0.11	4.293	4.799	0.686	3.019	10
Prdx1	N	1.938	0.172	0.03	0.089	0.349	1.674	2.214	0.196	−1.288	15
Prdx1	IH	2.147	0.116	0.013	0.054	0.181	1.977	2.318	0.314	−1.041	10
Prdx2	N	2.842	0.114	0.013	0.04	0.103	2.634	3.041	−0.207	−0.087	15
Prdx2	IH	2.918	0.063	0.004	0.021	0.121	2.82	2.984	−0.405	−1.432	10
Prdx3	N	5.156	0.186	0.034	0.036	0.288	4.845	5.483	−0.144	−0.671	15
Prdx3	IH	5.271	0.079	0.006	0.015	0.136	5.142	5.368	−0.545	−0.898	10
Prdx4	N	5.562	0.139	0.019	0.025	0.235	5.358	5.804	−0.05	−1.316	15
Prdx4	IH	5.468	0.203	0.041	0.037	0.305	5.247	5.853	0.599	−0.572	10
Prdx5	N	3.196	0.246	0.061	0.077	0.33	2.952	3.756	1.224	0.687	15
Prdx5	IH	3.351	0.092	0.009	0.028	0.141	3.216	3.502	−0.107	−0.543	10
Prdx6	N	4.149	0.231	0.053	0.056	0.43	3.915	4.614	0.783	−0.81	15
Prdx6	IH	4.186	0.134	0.018	0.032	0.226	3.942	4.366	−0.312	−0.544	10
Sod1	N	1.903	1.166	1.36	0.613	2.278	0.408	2.986	−0.448	−2.057	15
Sod1	IH	1.824	1.261	1.591	0.691	2.383	0.442	3.086	−0.013	−2.534	10
Sod2	N	3.618	0.787	0.619	0.218	1.606	2.385	4.62	−0.548	−1.343	15
Sod2	IH	3.29	1.075	1.156	0.327	2.111	2.18	4.353	−0.017	−2.534	10
Sod3	N	5.323	3.529	12.456	0.663	7.146	0.679	8.223	−0.486	−2.01	15
Sod3	IH	3.869	4.411	19.46	1.14	8.399	−1.451	8.214	−0.066	−2.427	10
Srxn1	N	5.171	0.814	0.662	0.157	1.675	4.018	5.978	−0.362	−1.946	15
Srxn1	IH	5.373	0.974	0.949	0.181	1.86	4.357	6.525	0.027	−2.466	10
Txnip	N	4.864	1.149	1.32	0.236	2.237	3.183	6.056	−0.423	−1.823	15
Txnip	IH	4.711	0.797	0.636	0.169	1.62	3.72	5.695	0.055	−1.849	10
Txnrd1	N	4.887	1.068	1.14	0.218	2.064	3.444	5.841	−0.467	−2.036	15
Txnrd1	IH	4.612	1.037	1.076	0.225	1.926	3.441	5.661	−0.014	−2.525	10
Txnrd3	N	7.398	0.954	0.91	0.129	1.987	6.152	8.284	−0.495	−1.907	15
Txnrd3	IH	6.36	1.563	2.444	0.246	2.7	3.966	7.973	−0.223	−1.983	10

Gene	Condition	Mean	SD	Variance	CoV	IQR	Min	Max	Skewness	Kurtosis	n
Cat	N	5.004	0.149	0.022	0.03	0.265	4.751	5.212	−0.148	−1.354	15
Cat	IH	5.114	0.092	0.008	0.018	0.187	4.965	5.22	−0.338	−1.354	10
Gpx1	N	4.231	0.167	0.028	0.04	0.159	3.98	4.586	0.88	0.871	15
Gpx1	IH	4.334	0.074	0.005	0.017	0.132	4.222	4.443	0.3	−0.807	10
Gpx3	N	6.32	0.251	0.063	0.04	0.304	6.01	6.796	0.788	−0.375	15
Gpx3	IH	6.303	0.15	0.022	0.024	0.307	6.099	6.498	0.118	−1.717	10
Gpx4	N	4.28	0.116	0.013	0.027	0.22	4.135	4.52	0.505	−0.436	15
Gpx4	IH	4.394	0.149	0.022	0.034	0.266	4.145	4.601	−0.296	−0.941	10
Gpx7	N	7.08	0.156	0.024	0.022	0.262	6.826	7.312	−0.274	−1.088	15
Gpx7	IH	7.319	0.203	0.041	0.028	0.355	7.09	7.681	0.452	−1.092	10
Gpx8	N	7.162	0.152	0.023	0.021	0.243	6.807	7.347	−0.691	0.312	15
Gpx8	IH	7.298	0.222	0.049	0.03	0.489	7.053	7.605	0.329	−1.575	10
Gsr	N	4.903	0.221	0.049	0.045	0.262	4.55	5.413	0.459	1.017	15
Gsr	IH	5.029	0.17	0.029	0.034	0.273	4.755	5.299	−0.3	−0.573	10
Gss	N	7.832	0.108	0.012	0.014	0.158	7.581	8.019	−0.757	0.953	15
Gss	IH	7.785	0.291	0.084	0.037	0.592	7.383	8.193	−0.154	−1.518	10
Gstk1	N	7.971	0.125	0.016	0.016	0.176	7.677	8.156	−0.676	0.787	15
Gstk1	IH	8.084	0.108	0.012	0.013	0.152	7.863	8.239	−0.778	0.746	10
Gstm1	N	4.838	0.133	0.018	0.028	0.166	4.51	4.985	−1.145	1.273	15
Gstm1	IH	4.518	0.127	0.016	0.028	0.11	4.293	4.799	0.686	3.019	10
Prdx1	N	1.938	0.172	0.03	0.089	0.349	1.674	2.214	0.196	−1.288	15
Prdx1	IH	2.147	0.116	0.013	0.054	0.181	1.977	2.318	0.314	−1.041	10
Prdx2	N	2.842	0.114	0.013	0.04	0.103	2.634	3.041	−0.207	−0.087	15
Prdx2	IH	2.918	0.063	0.004	0.021	0.121	2.82	2.984	−0.405	−1.432	10
Prdx3	N	5.156	0.186	0.034	0.036	0.288	4.845	5.483	−0.144	−0.671	15
Prdx3	IH	5.271	0.079	0.006	0.015	0.136	5.142	5.368	−0.545	−0.898	10
Prdx4	N	5.562	0.139	0.019	0.025	0.235	5.358	5.804	−0.05	−1.316	15
Prdx4	IH	5.468	0.203	0.041	0.037	0.305	5.247	5.853	0.599	−0.572	10
Prdx5	N	3.196	0.246	0.061	0.077	0.33	2.952	3.756	1.224	0.687	15
Prdx5	IH	3.351	0.092	0.009	0.028	0.141	3.216	3.502	−0.107	−0.543	10
Prdx6	N	4.149	0.231	0.053	0.056	0.43	3.915	4.614	0.783	−0.81	15
Prdx6	IH	4.186	0.134	0.018	0.032	0.226	3.942	4.366	−0.312	−0.544	10
Sod1	N	1.903	1.166	1.36	0.613	2.278	0.408	2.986	−0.448	−2.057	15
Sod1	IH	1.824	1.261	1.591	0.691	2.383	0.442	3.086	−0.013	−2.534	10
Sod2	N	3.618	0.787	0.619	0.218	1.606	2.385	4.62	−0.548	−1.343	15
Sod2	IH	3.29	1.075	1.156	0.327	2.111	2.18	4.353	−0.017	−2.534	10
Sod3	N	5.323	3.529	12.456	0.663	7.146	0.679	8.223	−0.486	−2.01	15
Sod3	IH	3.869	4.411	19.46	1.14	8.399	−1.451	8.214	−0.066	−2.427	10
Srxn1	N	5.171	0.814	0.662	0.157	1.675	4.018	5.978	−0.362	−1.946	15
Srxn1	IH	5.373	0.974	0.949	0.181	1.86	4.357	6.525	0.027	−2.466	10
Txnip	N	4.864	1.149	1.32	0.236	2.237	3.183	6.056	−0.423	−1.823	15
Txnip	IH	4.711	0.797	0.636	0.169	1.62	3.72	5.695	0.055	−1.849	10
Txnrd1	N	4.887	1.068	1.14	0.218	2.064	3.444	5.841	−0.467	−2.036	15
Txnrd1	IH	4.612	1.037	1.076	0.225	1.926	3.441	5.661	−0.014	−2.525	10
Txnrd3	N	7.398	0.954	0.91	0.129	1.987	6.152	8.284	−0.495	−1.907	15
Txnrd3	IH	6.36	1.563	2.444	0.246	2.7	3.966	7.973	−0.223	−1.983	10

Apoptosis

Gene	Condition	Mean	SD	Variance	CoV	IQR	Min	Max	Skewness	Kurtosis	n
Bax	N	5.054	0.244	0.06	0.048	0.371	4.523	5.421	−0.638	−0.085	15
Bax	IH	5.036	0.134	0.018	0.027	0.241	4.821	5.224	−0.245	−1.283	10
Bcl2	N	6.906	0.101	0.01	0.015	0.174	6.685	7.077	−0.471	0.244	15
Bcl2	IH	7.187	0.107	0.011	0.015	0.164	6.984	7.358	−0.305	0.261	10
Casp3	N	5.161	0.116	0.013	0.022	0.168	4.982	5.414	0.403	0.154	15
Casp3	IH	4.87	0.156	0.024	0.032	0.313	4.639	5.106	−0.015	−1.192	10
Casp9	N	8.567	0.248	0.061	0.029	0.422	8.204	8.969	0.353	−1.313	15
Casp9	IH	8.349	0.292	0.085	0.035	0.555	8.031	8.855	0.603	−0.974	10
Hif1a	N	4.789	0.161	0.026	0.034	0.279	4.458	4.988	−0.61	−0.485	15
Hif1a	IH	4.74	0.19	0.036	0.04	0.318	4.42	4.972	−0.291	−1.362	10
Parp1	N	5.799	0.176	0.031	0.03	0.3	5.491	6.044	−0.628	−0.781	15
Parp1	IH	6.081	0.157	0.025	0.026	0.312	5.931	6.31	0.517	−1.911	10

Gene	Condition	Mean	SD	Variance	CoV	IQR	Min	Max	Skewness	Kurtosis	n
Bax	N	5.054	0.244	0.06	0.048	0.371	4.523	5.421	−0.638	−0.085	15
Bax	IH	5.036	0.134	0.018	0.027	0.241	4.821	5.224	−0.245	−1.283	10
Bcl2	N	6.906	0.101	0.01	0.015	0.174	6.685	7.077	−0.471	0.244	15
Bcl2	IH	7.187	0.107	0.011	0.015	0.164	6.984	7.358	−0.305	0.261	10
Casp3	N	5.161	0.116	0.013	0.022	0.168	4.982	5.414	0.403	0.154	15
Casp3	IH	4.87	0.156	0.024	0.032	0.313	4.639	5.106	−0.015	−1.192	10
Casp9	N	8.567	0.248	0.061	0.029	0.422	8.204	8.969	0.353	−1.313	15
Casp9	IH	8.349	0.292	0.085	0.035	0.555	8.031	8.855	0.603	−0.974	10
Hif1a	N	4.789	0.161	0.026	0.034	0.279	4.458	4.988	−0.61	−0.485	15
Hif1a	IH	4.74	0.19	0.036	0.04	0.318	4.42	4.972	−0.291	−1.362	10
Parp1	N	5.799	0.176	0.031	0.03	0.3	5.491	6.044	−0.628	−0.781	15
Parp1	IH	6.081	0.157	0.025	0.026	0.312	5.931	6.31	0.517	−1.911	10

ROS Production

Gene	Condition	Mean	SD	Variance	CoV	IQR	Min	Max	Skewness	Kurtosis	n
Cox4i1	N	1.221	0.172	0.029	0.141	0.281	0.969	1.49	0.214	−1.114	15
Cox4i1	IH	1.356	0.138	0.019	0.102	0.172	1.055	1.537	−0.964	1.668	10
Fth1	N	0.885	0.182	0.033	0.205	0.319	0.523	1.121	−0.462	−0.86	15
Fth1	IH	1.238	0.115	0.013	0.093	0.219	1.065	1.425	0.328	−0.784	10
Hadh	N	6.106	0.223	0.05	0.037	0.376	5.78	6.471	0.401	−0.911	15
Hadh	IH	6.106	0.071	0.005	0.012	0.131	6.016	6.222	0.3	−1.148	10
Hmox1	N	7.867	0.406	0.165	0.052	0.139	6.485	8.209	−3.112	11.079	15
Hmox1	IH	7.338	0.677	0.458	0.092	0.498	5.566	7.973	−2.337	6.158	10
Idh1	N	3.495	0.114	0.013	0.033	0.167	3.3	3.662	−0.448	−0.912	15
Idh1	IH	3.366	0.11	0.012	0.033	0.171	3.166	3.487	−0.746	−0.492	10
Ndufv2	N	1.717	0.149	0.022	0.087	0.188	1.348	1.952	−0.876	1.445	15
Ndufv2	IH	1.892	0.112	0.012	0.059	0.144	1.664	2.052	−0.612	0.88	10
Nos1	N	6.622	0.184	0.034	0.028	0.242	6.162	6.834	−1.129	1.41	15
Nos1	IH	6.81	0.253	0.064	0.037	0.34	6.342	7.259	−0.027	0.776	10
Nqo1	N	9.003	0.22	0.048	0.024	0.359	8.646	9.36	0.129	−0.929	15
Nqo1	IH	8.994	0.145	0.021	0.016	0.218	8.745	9.151	−0.893	−0.265	10
Por	N	5.075	0.231	0.053	0.046	0.345	4.734	5.632	0.857	0.961	15
Por	IH	5.065	0.208	0.043	0.041	0.358	4.746	5.292	−0.52	−1.107	10

Gene	Condition	Mean	SD	Variance	CoV	IQR	Min	Max	Skewness	Kurtosis	n
Cox4i1	N	1.221	0.172	0.029	0.141	0.281	0.969	1.49	0.214	−1.114	15
Cox4i1	IH	1.356	0.138	0.019	0.102	0.172	1.055	1.537	−0.964	1.668	10
Fth1	N	0.885	0.182	0.033	0.205	0.319	0.523	1.121	−0.462	−0.86	15
Fth1	IH	1.238	0.115	0.013	0.093	0.219	1.065	1.425	0.328	−0.784	10
Hadh	N	6.106	0.223	0.05	0.037	0.376	5.78	6.471	0.401	−0.911	15
Hadh	IH	6.106	0.071	0.005	0.012	0.131	6.016	6.222	0.3	−1.148	10
Hmox1	N	7.867	0.406	0.165	0.052	0.139	6.485	8.209	−3.112	11.079	15
Hmox1	IH	7.338	0.677	0.458	0.092	0.498	5.566	7.973	−2.337	6.158	10
Idh1	N	3.495	0.114	0.013	0.033	0.167	3.3	3.662	−0.448	−0.912	15
Idh1	IH	3.366	0.11	0.012	0.033	0.171	3.166	3.487	−0.746	−0.492	10
Ndufv2	N	1.717	0.149	0.022	0.087	0.188	1.348	1.952	−0.876	1.445	15
Ndufv2	IH	1.892	0.112	0.012	0.059	0.144	1.664	2.052	−0.612	0.88	10
Nos1	N	6.622	0.184	0.034	0.028	0.242	6.162	6.834	−1.129	1.41	15
Nos1	IH	6.81	0.253	0.064	0.037	0.34	6.342	7.259	−0.027	0.776	10
Nqo1	N	9.003	0.22	0.048	0.024	0.359	8.646	9.36	0.129	−0.929	15
Nqo1	IH	8.994	0.145	0.021	0.016	0.218	8.745	9.151	−0.893	−0.265	10
Por	N	5.075	0.231	0.053	0.046	0.345	4.734	5.632	0.857	0.961	15
Por	IH	5.065	0.208	0.043	0.041	0.358	4.746	5.292	−0.52	−1.107	10

9.2 Models

Specifying the model to apply to each Gene’s DCq values:

Note

When there are several experiments (plates) for a Gene, a random intercept per Experiment is added.

model_OS <- function(dat) {
  contrasts(dat$Condition) <- contr.sum
  
  if (n_distinct(dat$Experiment) >= 2) {
    contrasts(dat$Experiment) <- contr.sum
    
    glmmTMB::glmmTMB(
      DCq ~ Condition + (1 | Experiment),
      family = gaussian("identity"),
      data = dat
    )
  }
  else {
    glmmTMB::glmmTMB(
      DCq ~ Condition,
      family = gaussian("identity"),
      data = dat
    )
  }
}

9.3 Effects Analysis

Computing p-values & contrasts for each Gene (based on Wald t-tests):

❖ Effects summary:

❖ Fold change plots:

Note

Only statistically significant genes are displayed.