Integrated Analysis of Hub Genes and Pathways In Esophageal Carcinoma Based on NCBI’s Gene Expression Omnibus (GEO) Database: A Bioinformatics Analysis

Tan Yu-jing; Tang Wen-jing; Tang Biao

doi:10.12659/MSM.923934

05 August 2020: Database Analysis

Integrated Analysis of Hub Genes and Pathways In Esophageal Carcinoma Based on NCBI’s Gene Expression Omnibus (GEO) Database: A Bioinformatics Analysis

Tan Yu-jing ^ACE , Tang Wen-jing ^C , Tang Biao ^AEG*

DOI: 10.12659/MSM.923934

Med Sci Monit 2020; 26:e923934

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Table 2 GO enrichment analysis of ESCA-related DEGs.

Category	Term	Annotation	Count	P Value	FDR
MF	GO: 0042393	Histone binding	5	0.040956	43.57063
	GO: 0004672	Protein kinase activity	9	0.037858	41.02474
	GO: 0017048	Rho GTPase binding	3	0.035287	38.83208
	GO: 0008083	Growth factor activity	6	0.029217	33.3507
	GO: 0003678	DNA helicase activity	3	0.026484	30.73641
	GO: 0042826	Histone deacetylase binding	5	0.023265	27.53669
	GO: 0019901	Protein kinase binding	10	0.019069	23.15887
	GO: 0016887	ATPase activity	7	0.013453	16.91675
	GO: 0048407	Platelet-derived growth factor binding	3	0.005775	7.618473
	GO: 0005201	Extracellular matrix structural constituent	5	0.005574	7.362384
	GO: 0005524	ATP binding	28	0.004315	5.745381
	GO: 0008574	ATP-dependent microtubule motor activity, plus-end-directed	4	7.15E-04	0.97331
	GO: 0008017	Microtubule binding	10	3.85E-04	0.525754
	GO: 0008201	Heparin binding	9	3.10E-04	0.423032
	GO: 0003777	Microtubule motor activity	7	2.05E-04	0.280292
	GO: 0005515	Protein binding	118	1.98E-04	0.271172
	GO: 0008307	Structural constituent of muscle	6	7.85E-05	0.107306
	GO: 0003779	Actin binding	15	1.63E-06	0.002223
CC	GO: 0005814	Centriole	5	0.034311	36.49999
	GO: 0097149	Centralspindlin complex	2	0.032082	34.56688
	GO: 0005694	Chromosome	5	0.0272	30.14128
	GO: 0070062	Extracellular exosome	42	0.0257	28.72761
	GO: 0005680	Anaphase-promoting complex	3	0.025342	28.38631
	GO: 0005584	Collagen type i trimer	2	0.021504	24.62943
	GO: 0016363	Nuclear matrix	5	0.021056	24.17972
	GO: 0051233	Spindle midzone	3	0.017618	20.64245
	GO: 0005925	Focal adhesion	11	0.010247	12.53825
	GO: 0015629	Actin cytoskeleton	8	0.009682	11.8868
	GO: 0005654	Nucleoplasm	44	0.008794	10.8543
	GO: 0005576	Extracellular region	29	0.008174	10.12583
	GO: 0048471	Perinuclear region of cytoplasm	15	0.007728	9.598831
	GO: 0005813	Centrosome	12	0.006822	8.519486
	GO: 0000922	Spindle pole	6	0.006621	8.277421
	GO: 0015630	Microtubule cytoskeleton	7	0.003771	4.795012
	GO: 0001725	Stress fiber	5	0.002747	3.514485
	GO: 0045120	Pronucleus	3	0.002356	3.021411
	GO: 0005737	Cytoplasm	77	0.001617	2.083603
	GO: 0005829	Cytosol	54	0.00154	1.984823
	GO: 0031012	Extracellular matrix	11	0.001477	1.904168
	GO: 0005876	Spindle microtubule	5	0.001282	1.655013
	GO: 0031262	Ndc80 complex	3	6.88E-04	0.890813
	GO: 0000942	Condensed nuclear chromosome Outer kinetochore	3	6.88E-04	0.890813
	GO: 0005874	Microtubule	12	5.90E-04	0.765086
	GO: 0030018	Z disc	8	2.97E-04	0.385939
	GO: 0005581	Collagen trimer	8	6.25E-05	0.081295
	GO: 0000776	Kinetochore	8	2.74E-05	0.035668
	GO: 0005871	Kinesin complex	7	2.22E-05	0.028929
	GO: 0005615	Extracellular space	33	2.02E-05	0.026247
	GO: 0005578	Proteinaceous extracellular matrix	14	7.32E-06	0.009524
	GO: 0005819	Spindle	10	6.68E-06	0.008694
	GO: 0000775	Chromosome, centromeric region	8	2.59E-06	0.003375
	GO: 0030496	Midbody	11	1.40E-06	0.001819
	GO: 0000777	Condensed chromosome kinetochore	11	3.37E-08	4.38E-05
BP	GO: 0007015	Actin filament organization	4	0.048188	55.68998
	GO: 0051436	Negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	4	0.046554	54.41983
	GO: 0001666	Response to hypoxia	6	0.046026	54.00186
	GO: 0046777	Protein autophosphorylation	6	0.046026	54.00186
	GO: 0044344	Cellular response to fibroblast growth factor stimulus	3	0.045033	53.20648
	GO: 2000660	Negative regulation of interleukin-1-mediated signaling pathway	2	0.044501	52.77484
	GO: 0010574	Regulation of vascular endothelial growth factor production	2	0.044501	52.77484
	GO: 0043154	Negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	4	0.043372	51.8463
	GO: 0097421	Liver regeneration	3	0.042339	50.98273
	GO: 0051384	Response to glucocorticoid	4	0.037348	46.59797
	GO: 0060326	Cell chemotaxis	4	0.037348	46.59797
	GO: 0007049	Cell cycle	7	0.037147	46.41426
	GO: 0045840	Positive regulation of mitotic nuclear division	3	0.034645	44.07219
	GO: 0071173	Spindle assembly checkpoint	2	0.033564	43.03115
	GO: 0060414	Aorta smooth muscle tissue morphogenesis	2	0.033564	43.03115
	GO: 0006977	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	4	0.033134	42.61195
	GO: 0000070	Mitotic sister chromatid segregation	3	0.032215	41.70664
	GO: 0006306	DNA methylation	3	0.032215	41.70664
	GO: 0042787	Protein ubiquitination involved in ubiquitin-dependent protein catabolic process	6	0.030104	39.57493
	GO: 0051966	Regulation of synaptic transmission, glutamatergic	3	0.02757	36.92013
	GO: 0051439	Regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	3	0.02757	36.92013
	GO: 0043547	Positive regulation of GTPase activity	13	0.027349	36.68291
	GO: 0070301	Cellular response to hydrogen peroxide	4	0.026698	35.9813
	GO: 1903779	Regulation of cardiac conduction	4	0.0255	34.66984
	GO: 0008283	Cell proliferation	10	0.023601	32.53933
	GO: 0048146	Positive regulation of fibroblast proliferation	4	0.023193	32.07322
	GO: 0000022	Mitotic spindle elongation	2	0.022502	31.27789
	GO: 0001501	Skeletal system development	6	0.019827	28.11186
	GO: 0010881	Regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ions	3	0.019192	27.33961
	GO: 0006939	Smooth muscle contraction	3	0.017299	24.99359
	GO: 0051726	Cell cycle regulation	6	0.013422	19.96503
	GO: 0031145	Anaphase-promoting complex-dependent catabolic process	5	0.012345	18.5125
	GO: 0006957	Complement activation, alternative pathway	3	0.009152	14.06012
	GO: 0051310	Metaphase plate congression	3	0.007801	12.10953
	GO: 0055119	Relaxation of cardiac muscle	3	0.007801	12.10953
	GO: 0048565	Digestive tract development	4	0.007152	11.1566
	GO: 0008284	Positive regulation of cell proliferation	13	0.006888	10.76681
	GO: 0030574	Collagen catabolic process	5	0.005947	9.363414
	GO: 0034501	Protein localization to kinetochore	3	0.005399	8.535467
	GO: 0032060	Bleb assembly	3	0.005399	8.535467
	GO: 0007019	Microtubule depolymerization	3	0.005399	8.535467
	GO: 0006268	DNA unwinding involved in DNA replication	3	0.005399	8.535467
	GO: 0009612	Response to mechanical stimulus	5	0.00445	7.087078
	GO: 0071549	Cellular response to dexamethasone stimulus	4	0.004196	6.694943
	GO: 0019221	Cytokine-mediated signaling pathway	7	0.003769	6.034147
	GO: 0032355	Response to estradiol	6	0.00373	5.973802
	GO: 0001558	Regulation of cell growth	6	0.00213	3.453634
	GO: 0000910	Cytokinesis	5	0.002095	3.397158
	GO: 0007094	Mitotic spindle assembly checkpoint	4	0.00141	2.299434
	GO: 0000086	G2/M transition of mitotic cell cycle	8	9.49E-04	1.552707
	GO: 0007080	Mitotic metaphase plate congression	5	7.83E-04	1.283031
	GO: 0007155	Cell adhesion	15	7.52E-04	1.232171
	GO: 0007018	Microtubule-based movement	7	3.11E-04	0.511889
	GO: 0030199	Collagen fibril organization	6	7.41E-05	0.122099
	GO: 0006936	Muscle contraction	9	2.91E-05	0.047888
	GO: 0007052	Mitotic spindle organization	6	1.99E-05	0.032833
	GO: 0000281	Mitotic cytokinesis	6	1.68E-05	0.027614
	GO: 0007059	Chromosome segregation	8	1.15E-05	0.018962
	GO: 0007062	Sister chromatid cohesion	12	2.35E-08	3.87E-05
	GO: 0007067	Mitotic nuclear division	20	5.66E-11	9.33E-08
	GO: 0051301	Cell division	25	1.55E-12	2.55E-09

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Integrated Analysis of Hub Genes and Pathways In Esophageal Carcinoma Based on NCBI’s Gene Expression Omnibus (GEO) Database: A Bioinformatics Analysis

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