Analysis of differentially expressed genes related to cerebral ischaemia in young rats based on the Gene Expression Omnibus database

Table 1 Sample information

Sample number	Strain	Gender	Rat age	Grouping	Sampling site
GSM5065037	SD rat	Male	March-April	Young MCAO	Brain tissue
GSM5065038	SD rat	Male	March-April	Young MCAO	Brain tissue
GSM5065039	SD rat	Male	March-April	Young MCAO	Brain tissue
GSM5065040	SD rat	Male	Eighteen-twenty months	Aged MCAO	Brain tissue
GSM5065041	SD rat	Male	Eighteen-twenty months	Aged MCAO	Brain tissue
GSM5065042	SD rat	Male	Eighteen-twenty months	Aged MCAO	Brain tissue

MCAO: Middle cerebral artery occlusion.

Table 2 Upregulated differential genes in young infarcted rats

ID	P value		t	B	logFC	Gene symbol
1367571_at	0.00000058	13.77		4.3557	1.55	Igf2
1387854_at	0.0000015	12.2		3.9423	1.714	Col1a2
1370155_at	0.00000306	11.14		3.5959	2.022	Col1a2
1371861_at	0.00000562	10.29		3.2741	1.547	Sfrp1
1374172_at	0.00001368	9.16		2.7581	1.51	Col8a2
1367592_at	0.00001669	8.92		2.6355	1.732	Tnnt2
1390450_at	0.00002515	8.45		2.3752	1.266	LOC100910855Ogn
1372299_at	0.00003639	8.03		2.1313	1.003	Cdkn1c
1392510_at	0.00004648	7.77		1.9652	1.255	Fam180a
1370391_at	0.0001211	6.81		1.2813	1.393	LOC100911902Crabp2
1370956_at	0.00012686	6.76		1.2468	1.051	Dcn
1390532_at	0.00014662	6.62		1.1385	1.399	Slc13a4
1388116_at	0.00016115	6.54		1.0672	1.085	Col1a1
1387197_at	0.00024297	6.16		0.7521	1.139	Omd
1370959_at	0.00052678	5.49		0.1359	1.321	Col3a1
1367700_at	0.00057972	5.42		0.0577	1.054	Fmod
1385248_at	0.00072166	5.24		-0.1224	2.301	LOC100910855Ogn
1385486_at	0.00072866	5.23		-0.1304	1.026	Bnc2
1367847_at	0.00093931	5.03		-0.3419	1.163	Nupr1
1373148_at	0.00122143	4.82		-0.5632	1.146	Cpxm2
1387306_at	0.00144695	4.69		-0.7073	1.666	Egr2
1390835_at	0.00176986	4.54		-0.8798	1.239	Slc47a1
1383263_at	0.00179702	4.53		-0.8929	1.539	LOC100910855Ogn

Table 3 Downregulated differential genes in young infarcted rats

ID	P value		t	B	logFC	Gene symbol
1374503_at	0.00000136	-12.35		3.9877	-1.314	Pbx3
1395359_at	0.00000867	-9.73		3.0291	-1.084	-
1390783_at	0.00001389	-9.14		2.7485	-1.025	Abca8a
1390052_at	0.00007757	-7.24		1.606	-1.015	LOC100912140
1373250_at	0.00008716	-7.13		1.5221	-1.12	Anln/Anlnl1
1396833_at	0.00067817	-5.29		-0.0711	-1.105	-
1368708_at	0.00068945	-5.27		-0.0847	-1.475	Drd2
1386931_at	0.00105762	-4.93		-0.4415	-1.465	Tnni3
1383516_at	0.00229766	-4.35		-1.1053	-1.138	Fgl2
1368478_at	0.00264936	-4.25		-1.2292	-1.061	Drd1
1368300_at	0.00271339	-4.23		-1.25	-1.206	Adora2a
1383578_at	0.00295369	-4.17		-1.3241	-1.017	LOC100911267Rad51

Table 4 Top 6 differentially up-regulated genes in young infarcted rats after adjustment of P value

ID	Adjusted P value	t	B	logFC	Gene symbol
1367571_at	0.0156	13.77	4.3557	1.55	Igf2
1387854_at	0.0156	12.2	3.9423	1.714	Col1a2
1370155_at	0.0238	11.14	3.5959	2.022	Col1a2
1371861_at	0.0291	10.29	3.2741	1.547	Sfrp1
1374172_at	0.0432	9.16	2.7581	1.51	Col8a2
1367592_at	0.0472	8.92	2.6355	1.732	Tnnt2

Table 5 Top 5 differential genes downregulated in young infarcted rats after adjustment of P value

ID	Adjusted P value	t	B	logFC	Gene symbol
1374503_at	0.0156	-12.35	3.9877	-1.314	Pbx3
1387450_at	0.0257	-10.71	3.4396	-0.922	Tgfa
1395359_at	0.0365	-9.73	3.0291	-1.084	-
1367695_at	0.0365	-9.63	2.9826	-0.976	Qdpr
1390783_at	0.0432	-9.14	2.7485	-1.025	Abca8

Two of the top 6 differentially expressed genes after adjustment of the P value were duplicated, and one of the top five downregulated differential genes was unnamed.

Table 6 Gene Ontology functional enrichment analysis of differential genes in young infarcted rats

GO	GO entry	GO description	Number of genes	P value
Biological process	GO:0042493	Drug reaction	6	5.21E-04
	GO:0001975	Response to amphetamine	3	0.001644593
	GO:0001568	Vascular development	3	0.003764749
	GO:0071230	Cellular response to amino acid stimulation	3	0.00430878
	GO:0006469	Negative regulation of protein kinase activity	3	0.007534713
	GO:0010579	Positive regulation of adenylate cyclase activity involved in G protein-coupled receptor signalling	2	0.01174588
	GO:0060158	Phospholipase C activates the dopamine receptor signalling pathway	2	0.01174588
	GO:0007212	Dopamine receptor signalling pathway	2	0.022075774
	GO:1900273	Positive regulation of long-term synaptic potentiation	2	0.023359725
	GO:0070208	Protein heterotrimer	2	0.025922792
	GO:0007190	Activation of adenylate cyclase activity	2	0.028479424
	GO:0051968	Positive regulation of glutamatergic synaptic transmission	2	0.033573445
	GO:0051482	Positive regulation of G protein-coupled cytosolic calcium concentration by phospholipase C activation	2	0.039905051
	GO:0048147	Negative regulation of fibroblast proliferation	2	0.043684948
Cellular composition	GO:0031012	Extracellular matrix	9	4.60E-10
	GO:0005578	Protein, extracellular matrix	7	5.09E-07
	GO:0005581	Collagen trimer	4	5.47E-05
	GO:0005584	Type I collagen trimer	2	0.002482326
	GO:0005861	Troponin complex	2	0.009893989
Molecular function	GO:0004952	Dopamine neurotransmitter receptor activity	2	0.006291172
	GO:0008144	Drug combination	3	0.00881302
	GO:0005515	Protein binding	7	0.011558726
	GO:0035240	Dopamine binding	2	0.013790827
	GO:0046872	Metal ion binding	6	0.025540723

For the convenience of typesetting, Table 6 only shows the enrichment analysis results of some important GO functions. GO: Gene Ontology.

Table 7 Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential genes in young infarcted rats

Entry	Patheway name	Number of genes	P value
rno04024	c-AMP signalling pathway	4	0.005710593
rno04512	ECM receptor interactions	3	0.012428441
rno04974	protein digestion and absorption	3	0.012428441
rno05146	amebiasis	3	0.019228955
rno04611	platelet activation	3	0.027273273
rno05012	Parkinson's disease	3	0.033955639
rno05034	alcoholism	3	0.044367858

c-AMP: Cyclic adenosine monophosphate; ECM: Extracellular matrix.