scholarly journals Data exploration tools for the Gene Ontology database

2004 ◽  
Vol 20 (18) ◽  
pp. 3442-3454 ◽  
Author(s):  
E. Shoop ◽  
P. Casaes ◽  
G. Onsongo ◽  
L. Lesnett ◽  
E. O. Petursdottir ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Data Exploration ◽  
Gene Ontology Database

scholarly journals Transcriptome Analysis of Testes and Uterus: Reproductive Dysfunction Induced by Toxoplasma gondii in Mice

2020 ◽  
Vol 8 (8) ◽  
pp. 1136
Author(s):  
Junjie Wang ◽  
Tanghui Liu ◽  
Yasser S. Mahmmod ◽  
Zipeng Yang ◽  
Jiexing Tan ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Toxoplasma Gondii ◽  
Acute Infection ◽  
The Other ◽  
Rna Seq ◽  
Mice Model ◽  
Reproductive Disorders ◽  
Kegg Database ◽  
Disease Pathogenesis ◽  
Differently Expressed Genes

Toxoplasma gondii (T. gondii) infection in female mammals during pregnancy can result in poor pregnancy. Similarly, it can result in male reproductive disorders in male mammals. Although the testes and uterus have very different biological makeup, they are still both attacked by T. gondii resulting in reproductive dysfunctions. We hypothesized that there are significant common genes in the testes and uterus that interact with T. gondii. Finding out and studying these genes is vital to understand the infection mechanism of T. gondii and the induced disease pathogenesis. To achieve this goal, we built a mice model of acute infection with T. gondii and the testes and uterus of the mice were sequenced by RNA-Seq. A total of 291 and 679 significantly differently expressed genes (DEGs) were obtained from the testes and the uterus, respectively. In the Gene Ontology (GO) analysis, part of the DEGs in the testes and uterus were related to 35 GO functions. When compared with the KEGG database, seven pathways affecting both the testes and uterus during the course of T. gondii infection were identified. In addition, Toxoplasmosis can significantly affect the expression of Nlrp5 and Insc leading to negative outcomes in the host. On the other hand, the host regulates Gbp7, Gbp2b, and Ifit3 to defend against T. gondii infection.

scholarly journals Characterization of Genomic Variation from Lotus (Nelumbo Adans.) Mutants with Wide and Narrow Tepals

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 593
Author(s):  
Fengluan Liu ◽  
Mi Qin ◽  
Shuo Li ◽  
Dasheng Zhang ◽  
Qingqing Liu ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Candidate Genes ◽  
Genomic Variation ◽  
Nucleotide Polymorphisms ◽  
Kegg Database ◽  
Water Lily ◽  
Single Nucleotide ◽  
Deletion Mutations ◽  
Variant Genes

Compared with rose, chrysanthemum, and water lily, the absence of short-wide and long-narrow tepals of ornamental lotus (Nelumbo Adans.) limits the commercial value of flowers. In this study, the genomes of two groups of lotus mutants with wide-short and narrow-long tepals were resequenced to uncover the genomic variation and candidate genes associated with tepal shape. In group NL (short for N. lutea, containing two mutants and one control of N. lutea), 716,656 single nucleotide polymorphisms (SNPs) and 221,688 insertion-deletion mutations (Indels) were obtained, while 639,953 SNPs and 134,6118 Indels were obtained in group WSH (short for ‘Weishan Hong’, containing one mutant and two controls of N. nucifera ‘Weishan Hong’). Only a small proportion of these SNPs and Indels was mapped to exonic regions of genome: 1.92% and 0.47%, respectively, in the NL group, and 1.66% and 0.48%, respectively, in the WSH group. Gene Ontology (GO) analysis showed that out of 4890 (NL group) and 1272 (WSH group) annotated variant genes, 125 and 62 genes were enriched (Q < 0.05), respectively. Additionally, in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 104 genes (NL group) and 35 genes (WSH group) were selected (p < 0.05). Finally, there were 306 candidate genes that were sieved to determine the development of tepal shape in lotus plants. It will be an essential reference for future identification of tepal-shaped control genes in lotus plants. This is the first comprehensive report of genomic variation controlling tepal shape in lotus, and the mutants in this study are promising materials for breeding novel lotus cultivars with special tepals.

The gene ontology and electro localization of ovine skin derived EST-SSR markers

2011 ◽  
Vol 33 (7) ◽  
pp. 731-737 ◽  
Author(s):  
Zun-Bao WANG ◽  
Zong-Sheng ZHAO ◽  
Peng YU ◽  
Hong-Bin WU ◽  
Qian BAN ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Ssr Markers

A Novel Prediction of Quaternary Structural Type of Proteins with Gene Ontology

2020 ◽  
Vol 27 (4) ◽  
pp. 313-320 ◽  
Author(s):  
Xuan Xiao ◽  
Wei-Jie Chen ◽  
Wang-Ren Qiu
Keyword(s):  
Gene Ontology ◽  
Feature Extraction ◽  
Extraction Method ◽  
Quaternary Structure ◽  
Structural Type ◽  
Sequence Information ◽  
Prediction System ◽  
Data Set ◽  
Feature Extraction Method ◽  
Prediction Rate

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.

Gene Ontology-Facilitated Genome Analysis

2003 ◽  
Vol 4 (7) ◽  
pp. 569-574
Author(s):  
Hanqing Xie
Keyword(s):  
Gene Ontology ◽  
Genome Analysis
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