Abstracting Genes to Gene Ontology Terms Allows Comparison across Multiple Species

2006 ◽  
Author(s):  
A. Kumar ◽  
M.A. Higgins ◽  
J.N. Calley ◽  
S.M. McAhren ◽  
B.W. Halstead ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Multiple Species

Drinking Animals: Sobriety, Intoxication and Interspecies Assemblages

2018 ◽  
Author(s):  
Gary Genosko
Keyword(s):  
American Literature ◽  
Ethanol Fermentation ◽  
Pure Form ◽  
Biological Factors ◽  
Multiple Species ◽  
Wine Bottle

While Deleuze explored the temporalities of alcoholism in American literature in The Logic of Sense, and Jean Clet Martin, among others, has extended this inquiry by further extracting the alcoholic’s lines of flight from the same literature, this chapter breaks the mould by understanding alcohol, distilled and in its pure form of ethanol, as well as its imbibition, as a question of a component that passes through anthropocentric, and across multiple non-anthropocentric assemblages. The exploitation of ethanol fermentation, for example, exists across species. Indeed, as we entertain more overtly human cultural examples, such as ‘wine’ for cats, a recent Japanese pet trend, the metabolic communion of interspecies companionship requires that the material expressivity of the substance is overcoded because the ‘wine’ is not only non-alcoholic but liquid catnip in a ‘wine’ bottle. Indeed, theorization of the pursuit of shared pleasures – using Guattari’s ethological terms, we might say deterritorializing from deterministic biological factors yet also modifying these in some measure as well (Machinic Unconscious) – and engaging multiple species is this chapter’s goal, achievable by plotting the passages of alcohol and its related components across assemblages and their material and socio-cultural expressive trajectories beyond strictly anthropocentric and Western prerogatives.

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

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

2019 ◽  
Vol 20 (13) ◽  
pp. 1147-1154 ◽  
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

<P>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. </P><P> 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&#039;UTR of Kruppel-like factor 2 (KLF2). </P><P> 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&#039;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. </P><P> 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.</P>

Network Pharmacology Approach uncovering Pathways involved in targeting Hsp90 through Curcumin and Epigallocatechin to control Inflammation.

2019 ◽  
Vol 16 ◽  
Author(s):  
Umme Hani ◽  
Shivananda Kandagalla ◽  
B.S. Sharath ◽  
K Jyothsna. ◽  
H Manjunatha.
Keyword(s):  
Gene Ontology ◽  
Molecular Chaperones ◽  
Curcuma Longa ◽  
Interaction Network ◽  
Network Pharmacology ◽  
Heme Oxygenase 1 ◽  
Nrf2 Pathway ◽  
Functional Behavior ◽  
Inflammatory Proteins ◽  
Prime Target

: Hsp90 are molecular chaperones of chronic inflammatory proteins and have emerged as prime target for treatment of inflammation. Principal components from Curcuma longa and Camellia sinensis, Curcumin and EGC respectively possesses anti-inflammatory properties inhibiting cytokines responsible for inflammation. Both act on common pathways in upregulation of heme oxygenase 1 through Pkcδ-Nrf2 pathway and downregulation of Tlr4, which in turn suppress expression of Hsp90. Curcumin and EGC were also found to bind -N and -C terminal domain of Hsp90 respectively. Based on this, work was designed with network pharmacological approach. Hsp90 associated gene targets of Curcumin and EGC were collected from databases, and gene ontology studies were done. PPI were obtained from string database for specific genes involved in Pkcδ-Nrf2 and Tlr4 pathway. Protein interaction network was constructed by cytoscape, and networks of Hsp90, Curcumin and EGC were merged to get common genes involved in Pkcδ-Nrf2 and Tlr4 pathway. Cluego analysis was done for obtained common genes to identify functional behavior in human diseases. Main proteins involved were identified as key regulators in Pkcδ-Nrf2 and Tlr4 pathway for controlling expression of Hsp90 from Curcumin and EGC in inflammation. Docking was performed on main proteins, Hsp90, Pkcδ and Tlr4 with Curcumin and EGC, significant binding energy was obtained for docked complexes. Combinatorial effects of Curcumin and EGC were observed in Pkcδ-Nrf2 and Tlr4pathway. Present study is an attempt to unravel common pathways mediated in intervention of Curcumin and EGC for suppression of Hsp90 associated with inflammation.

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