Ontological Analysis of Coronavirus Associated Human Genes at the COVID-19 Disease Portal

被引：1

作者：

Wang, Shur-Jen ^{[1
]}

Brodie, Kent C. ^{[2
]}

De Pons, Jeffrey L. ^{[1
]}

Demos, Wendy M. ^{[1
]}

Gibson, Adam C. ^{[1
]}

Hayman, G. Thomas ^{[1
]}

Hill, Morgan L. ^{[1
]}

Kaldunski, Mary L. ^{[1
]}

Lamers, Logan ^{[1
]}

Laulederkind, Stanley J. F. ^{[1
]}

Nalabolu, Harika S. ^{[1
]}

Thota, Jyothi ^{[1
]}

Thorat, Ketaki ^{[1
]}

Tutaj, Marek A. ^{[1
]}

Tutaj, Monika ^{[1
]}

Vedi, Mahima ^{[1
]}

Zacher, Stacy ^{[3
]}

Smith, Jennifer R. ^{[1
]}

Dwinell, Melinda R. ^{[4
]}

Kwitek, Anne E. ^{[4
]}

机构：

[1] Med Coll Wisconsin, Rat Genome Database, Dept Biomed Engn, Milwaukee, WI 53226 USA

[2] Med Coll Wisconsin, Clin & Translat Sci Inst, Milwaukee, WI 53226 USA

[3] Med Coll Wisconsin, Finance & Adm, Milwaukee, WI 53226 USA

[4] Med Coll Wisconsin, Rat Genome Database, Dept Physiol, Milwaukee, WI 53226 USA

来源：

GENES | 2022年 / 13卷 / 12期

关键词：

COVID-19; database; disease enrichment; liver disease; biological knowledgebase; gene set enrichment;

D O I：

10.3390/genes13122304

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The COVID-19 pandemic stemmed a parallel upsurge in the scientific literature about SARS-CoV-2 infection and its health burden. The Rat Genome Database (RGD) created a COVID-19 Disease Portal to leverage information from the scientific literature. In the COVID-19 Portal, gene-disease associations are established by manual curation of PubMed literature. The portal contains data for nine ontologies related to COVID-19, an embedded enrichment analysis tool, as well as links to a toolkit. Using these information and tools, we performed analyses on the curated COVID-19 disease genes. As expected, Disease Ontology enrichment analysis showed that the COVID-19 gene set is highly enriched with coronavirus infectious disease and related diseases. However, other less related diseases were also highly enriched, such as liver and rheumatic diseases. Using the comparison heatmap tool, we found nearly 60 percent of the COVID-19 genes were associated with nervous system disease and 40 percent were associated with gastrointestinal disease. Our analysis confirms the role of the immune system in COVID-19 pathogenesis as shown by substantial enrichment of immune system related Gene Ontology terms. The information in RGD's COVID-19 disease portal can generate new hypotheses to potentiate novel therapies and prevention of acute and long-term complications of COVID-19.

引用

页数：16

共 35 条

[1]

Ben Moftah Moayed, 2022, Health Sci Rev (Oxf), V2, P100011, DOI 10.1016/j.hsr.2021.100011

[2] QuickGO: a web-based tool for Gene Ontology searching [J].

Binns, David ;

Dimmer, Emily ;

Huntley, Rachael ;

Barrell, Daniel ;

O'Donovan, Claire ;

Apweiler, Rolf .

BIOINFORMATICS, 2009, 25 (22) :3045-3046

[3] Upregulation of the Chemokine (C-C Motif) Ligand 2 via a Severe Acute Respiratory Syndrome Coronavirus Spike-ACE2 Signaling Pathway [J].

Chen, I-Yin ;

Chang, Shin C. ;

Wu, Hung-Yi ;

Yu, Ting-Chun ;

Wei, Wen-Chin ;

Lin, Shiming ;

Chien, Chung-Liang ;

Chang, Ming-Fu .

JOURNAL OF VIROLOGY, 2010, 84 (15) :7703-7712

[4] Potential Pathophysiological Mechanisms Underlying Multiple Organ Dysfunction in Cytokine Release Syndrome [J].

Chen, Peixian ;

Tang, Yan ;

He, Weixin ;

Yang, Ruixuan ;

Lan, Zhien ;

Chen, Ruirong ;

Zhang, Peidong .

MEDIATORS OF INFLAMMATION, 2022, 2022

[5] Impaired coagulation, liver dysfunction and COVID-19: Discovering an intriguing relationship [J].

D'Ardes, Damiano ;

Boccatonda, Andrea ;

Cocco, Giulio ;

Fabiani, Stefano ;

Rossi, Ilaria ;

Bucci, Marco ;

Guagnano, Maria Teresa ;

Schiavone, Cosima ;

Cipollone, Francesco .

WORLD JOURNAL OF GASTROENTEROLOGY, 2022, 28 (11) :1102-1112

[6] Comparative Toxicogenomics Database (CTD): update 2021 [J].

Davis, Allan Peter ;

Grondin, Cynthia J. ;

Johnson, Robin J. ;

Sciaky, Daniela ;

Wiegers, Jolene ;

Wiegers, Thomas C. ;

Mattingly, Carolyn J. .

NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D1138-D1143

[7] Characterizing Long COVID: Deep Phenotype of a Complex Condition [J].

Deer, Rachel R. ;

Rock, Madeline A. ;

Vasilevsky, Nicole ;

Carmody, Leigh ;

Rando, Halie ;

Anzalone, Alfred J. ;

Basson, Marc D. ;

Bennett, Tellen D. ;

Bergquist, Timothy ;

Boudreau, Eilis A. ;

Bramante, Carolyn T. ;

Byrd, James Brian ;

Callahan, Tiffany J. ;

Chan, Lauren E. ;

Chu, Haitao ;

Chute, Christopher G. ;

Coleman, Ben D. ;

Davis, Hannah E. ;

Gagnier, Joel ;

Greene, Casey S. ;

Hillegass, William B. ;

Kavuluru, Ramakanth ;

Kimble, Wesley D. ;

Koraishy, Farrukh M. ;

Kohler, Sebastian ;

Liang, Chen ;

Liu, Feifan ;

Liu, Hongfang ;

Madhira, Vithal ;

Madlock-Brown, Charisse R. ;

Matentzoglu, Nicolas ;

Mazzotti, Diego R. ;

McMurry, Julie A. ;

McNair, Douglas S. ;

Moffitt, Richard A. ;

Monteith, Teshamae S. ;

Parker, Ann M. ;

Perry, Mallory A. ;

Pfaff, Emily ;

Reese, Justin T. ;

Saltz, Joel ;

Schuff, Robert A. ;

Solomonides, Anthony E. ;

Solway, Julian ;

Spratt, Heidi ;

Stein, Gary S. ;

Sule, Anupam A. ;

Topaloglu, Umit ;

Vavougios, George D. ;

Wang, Liwei .

EBIOMEDICINE, 2021, 74

[8]

Del Valle DM, 2020, NAT MED, V26, P1636, DOI [10.1101/2020.05.28.20115758, 10.1038/s41591-020-1051-9]

[9] Clinical features and predictive factors related to liver injury in SARS-CoV-2 Delta and Omicron variant-infected patients [J].

Deng, Haohui ;

Lin, Haowei ;

Mai, Yuzhen ;

Liu, Huiyuan ;

Chen, Weilie .

EUROPEAN JOURNAL OF GASTROENTEROLOGY & HEPATOLOGY, 2022, 34 (09) :933-939

[10] Clinical Characteristics of Coronavirus Disease 2019 in China [J].

Guan, W. ;

Ni, Z. ;

Hu, Yu ;

Liang, W. ;

Ou, C. ;

He, J. ;

Liu, L. ;

Shan, H. ;

Lei, C. ;

Hui, D. S. C. ;

Du, B. ;

Li, L. ;

Zeng, G. ;

Yuen, K. -Y. ;

Chen, R. ;

Tang, C. ;

Wang, T. ;

Chen, P. ;

Xiang, J. ;

Li, S. ;

Wang, Jin-lin ;

Liang, Z. ;

Peng, Y. ;

Wei, L. ;

Liu, Y. ;

Hu, Ya-hua ;

Peng, P. ;

Wang, Jian-ming ;

Liu, J. ;

Chen, Z. ;

Li, G. ;

Zheng, Z. ;

Qiu, S. ;

Luo, J. ;

Ye, C. ;

Zhu, S. ;

Zhong, N. .

NEW ENGLAND JOURNAL OF MEDICINE, 2020, 382 (18) :1708-1720

← 1 2 3 4 →