Differential effect of mild and severe pulmonary embolism on the rat lung transcriptome

Zagorski, John; Kline, Jeffrey A.

doi:10.1186/s12931-016-0405-9

Respiratory Research

Table 1 DAVID Functional Annotation Charts, 2-h and 18-h Mild PE verses Vehicle

From: Differential effect of mild and severe pulmonary embolism on the rat lung transcriptome

Category	Term	^a2-h Mild-PE vs. Vehicle					18-h Mild-PE vs. Vehicle
Category	Term	Ct	%	Dir	Fold	B&H	Ct	%	Dir	Fold	B&H
SP_PIR	acetylation						78	14.03	UP	1.51	0.009
*rno04920*	*Adipocytokine signaling pathway*	6	*2.93*	UP	*7.47*	*0.015*
rno00970	Aminoacyl-tRNA biosynthesis						8	1.44	UP	5.56	0.017
*rno04210*	*Apoptosis*	6	*2.93*	UP	*5.89*	*0.028*
rno00330	Arginine and proline metabolism						9	1.62	UP	4.72	0.015
rno05217	Basal cell carcinoma						10	1.11	D	4.28	0.016
IPR004827	Basic-leucine zipper (bZIP) transcription factor	7	3.41	UP	11.97	0.003
SM00338	BRLZ	7	3.41	UP	10.46	0.001
*rno04062*	*Chemokine signaling pathway*	12	*5.85*	UP	*5.85*	*0.000*	20	*3.60*	UP	*3.25*	*0.001*
SP_PIR	chemotaxis	9	4.39	UP	22.67	0.000	11	1.98	UP	10.30	0.000
rno04610	Complement and coagulation cascades						10	1.80	UP	3.97	0.019
SP_PIR	cytokine	11	5.37	UP	9.02	0.000	16	2.88	UP	4.88	0.000
*rno04060*	*Cytokine-cytokine receptor interaction*	10	*4.88*	UP	*4.24*	*0.008*	23	*4.14*	UP	*3.25*	*0.000*
*rno04623*	*Cytosolic DNA-sensing pathway*	5	*2.44*	UP	*9.07*	*0.024*
*SP_PIR*	*disulfide bond*						76	*13.67*	UP	*1.43*	*0.044*
SP_PIR	dna-binding	20	9.76	UP	2.43	0.023
rno00982	Drug metabolism						13	1.45	D	3.94	0.004
rno04512	ECM-receptor interaction						14	1.56	D	3.77	0.005
PIRSF001719	fos transforming protein	4	1.95	UP	59.84	0.001
IPR000837	Fos transforming protein	4	1.95	UP	40.08	0.010
rno00480	Glutathione metabolism						9	1.00	D	3.93	0.042
*rno04640*	*Hematopoietic cell lineage*	6	*2.93*	UP	*6.42*	*0.022*
rno00340	Histidine metabolism						7	0.78	D	6.37	0.017
SP_PIR	inflammatory response	8	3.90	UP	16.01	0.000	11	1.98	UP	8.18	0.000
*rno04010*	*MAPK signaling pathway*	10	*4.88*	UP	*3.14*	*0.029*
rno00980	Metabolism of xenobiotics by cytochrome P450						13	1.45	D	4.73	0.002
rno04621	NOD-like receptor signaling pathway	9	4.39	UP	12.11	0.000	10	1.80	UP	4.49	0.016
*SP_PIR*	*oxidoreductase*						42	*4.68*	D	*1.89*	*0.034*
*rno05020*	*Prion diseases*						7	*1.26*	UP	*5.56*	*0.028*
SP_PIR	ribosome biogenesis						7	1.26	UP	8.85	0.007
SM00199	SCY	8	3.90	UP	16.89	0.000	10	1.80	UP	8.76	0.000
*IPR000827*	*Small chemokine, C-C group, conserved site*	4	*1.95*	UP	*25.50*	*0.033*
IPR001811	Small chemokine, interleukin-8-like	8	3.90	UP	19.35	0.000	10	1.80	UP	8.70	0.001
*PIRSF001950*	*small inducible chemokine, C/CC types*	5	*2.44*	UP	*24.93*	*0.001*
*rno04620*	*Toll-like receptor signaling pathway*	9	*4.39*	UP	*8.34*	*0.000*

Functional annotations significantly over-represented in the lists of up-regulated and down-regulated genes during 2-h and 18-h Low-PE. Annotations unique to Low-PE are highlighted in bold italics; annotations common to Low-PE and High-PE (Table 2) are in standard font. Key: “Ct.”, number genes from a GeneSifter pairwise t-test result (Additional file 3A-C) that were present in the functional annotation indicated; “%”, percent of genes contained within a list that were present in an annotation; “Dir, UP”, annotations that were identified by DAVID when up-regulated genes were used as the search query; “Dir, D”, annotations that were identified by DAVID when down-regulated genes were used as the search query. “Fold”, expression relative to vehicle group; B&H, value of Benjamini and Hochberg adjustment for false discovery following t-test. ^aNo 2-h DOWN annotations meet B&H < 0.05

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