Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

Khan, Yusuf; Hammarström, Daniel; Rønnestad, Bent R.; Ellefsen, Stian; Ahmad, Rafi

doi:10.1186/s12859-020-03866-y

BMC Bioinformatics

Table 4 Functional annotation analysis of time−dependent effects of acute resistance exercise

From: Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

Gene ontology category	ID	Description	Rank P-value	Gene−set enrichment analysis (GSEA)		ORA P-value
Gene ontology category	ID	Description	Rank P-value	GSEA P-value	NES	ORA P-value
Biological process	GO:0050900	Leukocyte migration	2.31e−16	0.010	1.58	1.04e−04
	GO:0009617	Response to bacterium	6.61e−14	1.42e−04	1.81	8.54e−06
	GO:0060326	Cell chemotaxis	6.69e−14	0.019	1.61	1.15e−04
	GO:0006954	Inflammatory response	2.08e−12	0.019	1.45	0.048
	GO:0002237	Response to molecule of bacterial origin	2.08e−12	4.61e−05	2.04	2.29e−05
	GO:0042330	Taxis	1.11e−11	9.24e−04	1.68	3.05e−05
	GO:0007159	Leukocyte cell cell adhesion	1.17e−11	0.003	1.78	4.02e−04
	GO:0030595	Leukocyte chemotaxis	8.29e−11	0.038	1.54	0.004
	GO:0048514	Blood vessel morphogenesis	8.72e−11	1.20e−05	1.89	1.78e−11
	GO:0042110	T cell activation	1.25e−09	0.022	1.46	6.84e−04
Cellular component	GO:0072562	Blood microparticle	3.23e−04	0.726	1.20	NA
	GO:0098589	Membrane region	0.004	0.162	1.39	NA
	GO:0042581	Specific granule	0.009	0.644	1.18	NA
	GO:0070820	Tertiary granule	0.055	0.444	1.28	NA
	GO:0005667	Transcription factor complex	0.070	1.93e−04	1.88	NA
	GO:0000932	P body	0.082	0.243	1.49	0.049
	GO:1903293	Phosphatase complex	0.095	0.012	1.97	0.049
	GO:0030055	Cell substrate junction	0.110	0.033	1.49	NA
	GO:0051233	Spindle midzone	0.116	0.647	1.29	NA
	GO:1904724	Tertiary granule lumen	0.180	0.091	1.81	NA
Molecular function	GO:0001216	DNA binding transcription activator activity	8.87e−15	1.50e−14	2.56	NA
	GO:0035326	Cis regulatory region binding	7.65e−10	3.00e−15	2.38	0.035
	GO:0030545	Receptor regulator activity	3.34e−07	0.004	1.75	0.003
	GO:0005125	Cytokine activity	8.04e−07	0.002	2.00	0.004
	GO:0001217	DNA binding transcription repressor activity	2.71e−06	6.07e−04	1.89	NA
	GO:0001968	Fibronectin binding	3.90e−05	0.411	1.30	0.024
	GO:0001664	G protein coupled receptor binding	3.90e−05	0.078	1.52	0.047
	GO:0008083	Growth factor activity	4.22e−05	0.001	2.03	0.004
	GO:0005126	Cytokine receptor binding	2.11e−04	9.14e−04	1.94	0.047
	GO:0140272	Exogenous protein binding	3.80e−04	0.198	1.54	NA
Biological process	GO:0043062	Extracellular structure organization	1.21e−11	0.006	− 1.57	0.046
	GO:0001501	Skeletal system development	6.32e−09	0.057	− 1.32	0.008
	GO:0072676	Lymphocyte migration	3.54e−07	0.126	− 1.42	NA
	GO:0032963	Collagen metabolic process	1.43e−06	0.032	− 1.61	NA
	GO:0002697	Regulation of immune effector process	1.60e−06	0.115	− 1.31	NA
	GO:0002250	Adaptive immune response	6.08e−06	0.023	− 1.43	NA
	GO:0070661	Leukocyte proliferation	6.23e−06	0.055	− 1.40	NA
	GO:0060348	Bone development	7.92e−06	0.031	− 1.49	NA
	GO:0042098	T cell proliferation	1.68e−05	0.127	− 1.34	NA
	GO:0033627	Cell adhesion mediated by integrin	1.69e−05	0.288	− 1.27	0.007
Cellular component	GO:0031012	Extracellular matrix	8.06e−15	7.19e−11	− 2.12	NA
	GO:0062023	Collagen containing extracellular matrix	8.74e−12	3.62e−13	− 2.29	NA
	GO:0005581	Collagen trimer	3.23e−04	7.19e−11	− 2.56	NA
	GO:0009897	ExteRNAl side of plasma membrane	0.001	0.023	− 1.57	NA
	GO:0005788	Endoplasmic reticulum lumen	0.008	0.003	− 1.69	NA
	GO:0098552	Side of membrane	0.012	0.460	− 1.18	NA
	GO:0043235	Receptor complex	0.014	0.210	− 1.29	NA
	GO:0043202	Lysosomal lumen	0.032	0.002	− 1.91	NA
	GO:0035579	Specific granule membrane	0.065	0.839	− 1.09	NA
	GO:0098802	Plasma membrane signaling receptor complex	0.092	0.263	− 1.37	NA
Molecular function	GO:0005201	Extracellular matrix structural constituent	2.40e−07	6.68e−10	− 2.38	NA
	GO:0005539	Glycosaminoglycan binding	1.38e−06	0.251	− 1.27	0.048
	GO:0008201	Heparin binding	7.60e−06	0.224	− 1.33	NA
	GO:0005178	Integrin binding	7.04e−04	0.103	− 1.42	NA
	GO:1901681	Sulfur compound binding	8.19e−04	0.098	− 1.35	NA
	GO:0030246	Carbohydrate binding	8.22e−04	0.230	− 1.27	NA
	GO:0005518	Collagen binding	0.004	0.050	− 1.66	NA
	GO:0043394	Proteoglycan binding	0.010	0.185	− 1.53	NA
	GO:0050840	Extracellular matrix binding	0.011	0.351	− 1.27	NA
	GO:0019838	Growth factor binding	0.016	0.195	− 1.35	NA

^aRank-based enrichment test based on minimum significant difference identifies gene−sets that are over-represented among top-ranked genes without a directional hypothesis
^bGene−set enrichment analysis (GSEA) tests for over-representation in among top and bottom genes based on Log₂ fold-changes in comparing time−points (Post- vs. Pre−exercise). Positive normalized enrichment scores (NES) indicate genes with higher expression Post- compared to Pre−exercise, negative NES indicates genes with higher expression Pre− compared to Post-exercise
^cOver-representation tests based on differentially expressed genes. P-values are adjusted for FDR

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