Data exploration tools for the Gene Ontology database

Background: The information of quaternary structure attributes of proteins is very important because it is closely related to the biological functions of proteins. With the rapid development of new generation sequencing technology, we are facing a challenge: how to automatically identify the four-level attributes of new polypeptide chains according to their sequence information (i.e., whether they are formed as just as a monomer, or as a hetero-oligomer, or a homo-oligomer). Objective: In this article, our goal is to find a new way to represent protein sequences, thereby improving the prediction rate of protein quaternary structure. Methods: In this article, we developed a prediction system for protein quaternary structural type in which a protein sequence was expressed by combining the Pfam functional-domain and gene ontology. turn protein features into digital sequences, and complete the prediction of quaternary structure through specific machine learning algorithms and verification algorithm. Results: Our data set contains 5495 protein samples. Through the method provided in this paper, we classify proteins into monomer, or as a hetero-oligomer, or a homo-oligomer, and the prediction rate is 74.38%, which is 3.24% higher than that of previous studies. Through this new feature extraction method, we can further classify the four-level structure of proteins, and the results are also correspondingly improved. Conclusion: After the applying the new prediction system, compared with the previous results, we have successfully improved the prediction rate. We have reason to believe that the feature extraction method in this paper has better practicability and can be used as a reference for other protein classification problems.

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Gene Ontology-Facilitated Genome Analysis

Current Genomics ◽

10.2174/1389202033490196 ◽

2003 ◽

Vol 4 (7) ◽

pp. 569-574

Author(s):

Hanqing Xie

Keyword(s):

Gene Ontology ◽

Genome Analysis

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Overexpression of miR-340-5p Inhibits Skin Fibroblast Proliferation by Targeting Kruppel-like Factor 2

Current Pharmaceutical Biotechnology ◽

10.2174/1389201020666190725112304 ◽

2019 ◽

Vol 20 (13) ◽

pp. 1147-1154 ◽

Cited By ~ 2

Author(s):

Ling Chen ◽

Qian Li ◽

Xun Lu ◽

Xiaohua Dong ◽

Jingyun Li

Keyword(s):

Gene Ontology ◽

Skin Fibroblast ◽

Kegg Pathway ◽

Normal Skin ◽

Skin Fibroblasts ◽

Differentially Expressed ◽

Luciferase Reporter ◽

Fibroblast Proliferation ◽

Pathway Analyses ◽

Normal Skin Fibroblast

Objective: MicroRNA (miR)-340-5p has been identified to play a key role in several cancers. However, the function of miR-340-5p in skin fibroblasts remains largely unknown. Methods: Gain of function experiments were performed by infecting normal skin fibroblast cells with a lentivirus carrying 22-bp miR-340-5p. Cell proliferation was detected by Cell Counting Kit-8 (CCK-8) assay. To uncover the mechanisms, mRNA-seq was used. Differentially expressed mRNAs were further determined by Gene Ontology and KEGG pathway analyses. The protein levels were analysed by Western blotting. A dual-luciferase reporter assay was used to detect the direct binding of miR-340-5p with the 3'UTR of Kruppel-like factor 2 (KLF2). Results: MiR-340-5p lentivirus infection suppressed normal skin fibroblast proliferation. The mRNAseq data revealed that 41 mRNAs were differentially expressed, including 22 upregulated and 19 downregulated transcripts in the miR-340-5p overexpression group compared with those in the control group. Gene Ontology and KEGG pathway analyses revealed that miR-340-5p overexpression correlated with the macromolecule biosynthetic process, cellular macromolecule biosynthetic process, membrane, and MAPK signalling pathway. Bioinformatics analysis and luciferase reporter assays showed that miR-340-5p binds to the 3'UTR of KLF2. Forced expression of miR-340-5p decreased the expression of KLF2 in normal skin fibroblasts. Overexpression of KLF2 restored skin fibroblast proliferation in the miR-340-5p overexpression group. Conclusion: This study demonstrates that miR-340-5p may suppress skin fibroblast proliferation, possibly through targeting KLF2. These findings could help us understand the function of miR-340-5p in skin fibroblasts. miR-340-5p could be a therapeutic target for preventing scarring.

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