scholarly journals Predicting lncRNA–Protein Interaction With Weighted Graph-Regularized Matrix Factorization

2021 ◽  
Vol 12 ◽  
Author(s):  
Xibo Sun ◽  
Leiming Cheng ◽  
Jinyang Liu ◽  
Cuinan Xie ◽  
Jiasheng Yang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Matrix Factorization ◽  
Experimental Validation ◽  
Matrix Protein ◽  
Biological Activities ◽  
Weighted Graph ◽  
Similarity Matrix ◽  
Non Coding Rnas ◽  
Accuracy Performance

Long non-coding RNAs (lncRNAs) are widely concerned because of their close associations with many key biological activities. Though precise functions of most lncRNAs are unknown, research works show that lncRNAs usually exert biological function by interacting with the corresponding proteins. The experimental validation of interactions between lncRNAs and proteins is costly and time-consuming. In this study, we developed a weighted graph-regularized matrix factorization (LPI-WGRMF) method to find unobserved lncRNA–protein interactions (LPIs) based on lncRNA similarity matrix, protein similarity matrix, and known LPIs. We compared our proposed LPI-WGRMF method with five classical LPI prediction methods, that is, LPBNI, LPI-IBNRA, LPIHN, RWR, and collaborative filtering (CF). The results demonstrate that the LPI-WGRMF method can produce high-accuracy performance, obtaining an AUC score of 0.9012 and AUPR of 0.7324. The case study showed that SFPQ, SNHG3, and PRPF31 may associate with Q9NUL5, Q9NUL5, and Q9UKV8 with the highest linking probabilities and need to further experimental validation.

scholarly journals The biogenesis and biological function of PIWI-interacting RNA in cancer

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Silu Chen ◽  
Shuai Ben ◽  
Junyi Xin ◽  
Shuwei Li ◽  
Rui Zheng ◽  
...  
Keyword(s):  
Cancer Diagnosis ◽  
Precancerous Lesions ◽  
Biological Activities ◽  
Cancer Hallmarks ◽  
Diagnosis And Prognosis ◽  
Small Ncrnas ◽  
Bioinformatics Databases ◽  
Non Coding Rnas ◽  
Underlying Mechanisms ◽  
Proliferative Signaling

AbstractSmall non-coding RNAs (ncRNAs) are vital regulators of biological activities, and aberrant levels of small ncRNAs are commonly found in precancerous lesions and cancer. PIWI-interacting RNAs (piRNAs) are a novel type of small ncRNA initially discovered in germ cells that have a specific length (24–31 nucleotides), bind to PIWI proteins, and show 2′-O-methyl modification at the 3′-end. Numerous studies have revealed that piRNAs can play important roles in tumorigenesis via multiple biological regulatory mechanisms, including silencing transcriptional and posttranscriptional gene processes and accelerating multiprotein interactions. piRNAs are emerging players in the malignant transformation of normal cells and participate in the regulation of cancer hallmarks. Most of the specific cancer hallmarks regulated by piRNAs are involved in sustaining proliferative signaling, resistance to cell death or apoptosis, and activation of invasion and metastasis. Additionally, piRNAs have been used as biomarkers for cancer diagnosis and prognosis and have great potential for clinical utility. However, research on the underlying mechanisms of piRNAs in cancer is limited. Here, we systematically reviewed recent advances in the biogenesis and biological functions of piRNAs and relevant bioinformatics databases with the aim of providing insights into cancer diagnosis and clinical applications. We also focused on some cancer hallmarks rarely reported to be related to piRNAs, which can promote in-depth research of piRNAs in molecular biology and facilitate their clinical translation into cancer treatment.

scholarly journals Spread of Epidemic Disease on Edge-Weighted Graphs from a Database: A Case Study of COVID-19

2021 ◽  
Vol 18 (9) ◽  
pp. 4432
Author(s):  
Ronald Manríquez ◽  
Camilo Guerrero-Nancuante ◽  
Felipe Martínez ◽  
Carla Taramasco
Keyword(s):  
Public Health ◽  
Infectious Diseases ◽  
Preventive Measures ◽  
Weighted Graph ◽  
Real Data ◽  
Sir Model ◽  
Weighted Graphs ◽  
Epidemic Disease ◽  
The Real

The understanding of infectious diseases is a priority in the field of public health. This has generated the inclusion of several disciplines and tools that allow for analyzing the dissemination of infectious diseases. The aim of this manuscript is to model the spreading of a disease in a population that is registered in a database. From this database, we obtain an edge-weighted graph. The spreading was modeled with the classic SIR model. The model proposed with edge-weighted graph allows for identifying the most important variables in the dissemination of epidemics. Moreover, a deterministic approximation is provided. With database COVID-19 from a city in Chile, we analyzed our model with relationship variables between people. We obtained a graph with 3866 vertices and 6,841,470 edges. We fitted the curve of the real data and we have done some simulations on the obtained graph. Our model is adjusted to the spread of the disease. The model proposed with edge-weighted graph allows for identifying the most important variables in the dissemination of epidemics, in this case with real data of COVID-19. This valuable information allows us to also include/understand the networks of dissemination of epidemics diseases as well as the implementation of preventive measures of public health. These findings are important in COVID-19’s pandemic context.

Fast and Low Memory Cost Matrix Factorization: Algorithm, Analysis, and Case Study

2020 ◽  
Vol 32 (2) ◽  
pp. 288-301
Author(s):  
Yan Yan ◽  
Mingkui Tan ◽  
Ivor W. Tsang ◽  
Yi Yang ◽  
Qinfeng Shi ◽  
...  
Keyword(s):  
Matrix Factorization ◽  
Algorithm Analysis ◽  
Cost Matrix ◽  
Factorization Algorithm ◽  
Memory Cost

scholarly journals A case study on in vitro investigations of the potent biological activities of wheat germ and black cumin seed oil

2015 ◽  
Vol 39 ◽  
pp. 801-812 ◽  
Author(s):  
Didem AĞ ŞELECİ ◽  
Zinar Pınar GÜMÜŞ ◽  
Murat YAVUZ ◽  
Muharrem ŞELECİ ◽  
Rebecca BONGARTZ ◽  
...  
Keyword(s):  
Wheat Germ ◽  
Seed Oil ◽  
Biological Activities ◽  
Black Cumin ◽  
Black Cumin Seed ◽  
Cumin Seed ◽  
Black Cumin Seed Oil

scholarly journals A Bibliometric Analysis of Researches on Flap Endonuclease 1 From 2005 to 2019

2021 ◽  
Author(s):  
Qiaochu Wei ◽  
Jiming Shen ◽  
Dongni Wang ◽  
Xu Han ◽  
Jing Shi ◽  
...  
Keyword(s):  
Bibliometric Analysis ◽  
Protein Interactions ◽  
Cell Biology ◽  
Biological Activities ◽  
The United States ◽  
Dna Metabolism ◽  
Flap Endonuclease 1 ◽  
The Past ◽  
Oncology Research ◽  
Research Frontiers

Abstract Background: Flap endonuclease 1 (FEN1) is a structure-specific nuclease that plays a role in a variety of DNA metabolism processes. FEN1 is important for maintaining genomic stability and regulating cell growth and development. It is associated with the occurrence and development of several diseases, especially cancers. There is a lack of systematic bibliometric analyses focusing on research trends and knowledge structures related to FEN1.Purpose: To analyze hotspots, the current state and research frontiers performed for FEN1 over the past 15 years. Methods: Publications were retrieved from the Web of Science Core Collection (WoSCC) database, analyzing publication dates ranging from 2005 to 2019. VOSviewer1.6.15 and Citespace5.7 R1 were used to perform a bibliometric analysis in terms of countries, institutions, authors, journals and research areas related to FEN1. A total of 421 publications were included in this analysis. Results: Our findings indicated that FEN1 has received more attention and interest from researchers in the past 15 years. Institutes in the United States, specifically the Beckman Research Institute of City of Hope published the most research related to FEN1. SHEN BH，ZHENG L and BAMBARA RA were the most active researchers investigating this endonuclease and most of this research was published in the Journal of Biological Chemistry. The main scientific areas of FEN1 were related to biochemistry, molecular biology，cell biology，genetics and oncology. Research hotspots included biological activities, DNA metabolism mechanisms, protein-protein interactions and gene mutations. Research frontiers included oxidative stress, phosphorylation and tumor progression and treatment. Conclusion: This bibliometric study may aid researchers in the understanding of the knowledge base and research frontiers associated with FEN1. In addition, emerging hotspots for research can be used as the subjects of future studies.

scholarly journals Long noncoding RNAs: fine-tuners hidden in the cancer signaling network

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Shanshan Zhao ◽  
Xue Zhang ◽  
Shuo Chen ◽  
Song Zhang
Keyword(s):  
Signaling Pathways ◽  
Cancer Progression ◽  
Biological Activities ◽  
Noncoding Rnas ◽  
Fine Tuning ◽  
Multiple Perspectives ◽  
Sequencing Technology ◽  
Protein Coding ◽  
Abnormal Signal ◽  
Non Coding Rnas

AbstractWith the development of sequencing technology, a large number of long non-coding RNAs (lncRNAs) have been identified in addition to coding genes. LncRNAs, originally considered as junk RNA, are dysregulated in various types of cancer. Although protein-coding signaling pathways underlie various biological activities, and abnormal signal transduction is a key trigger and indicator for tumorigenesis and cancer progression, lncRNAs are sparking keen interest due to their versatile roles in fine-tuning signaling pathways. We are just beginning to scratch the surface of lncRNAs. Therefore, despite the fact that lncRNAs drive malignant phenotypes from multiple perspectives, in this review, we focus on important signaling pathways modulated by lncRNAs in cancer to demonstrate an up-to-date understanding of this emerging field.

scholarly journals Triptolide Modulates the Expression of Inflammation-Associated lncRNA-PACER and lincRNA-p21 in Mycobacterium tuberculosis–Infected Monocyte-Derived Macrophages

2021 ◽  
Vol 12 ◽  
Author(s):  
Ousman Tamgue ◽  
Julius Ebua Chia ◽  
Frank Brombacher
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Target Genes ◽  
Cell Function ◽  
Immune Cell ◽  
Biological Activities ◽  
Target Cells ◽  
Dependent Manner ◽  
Direct Targeting ◽  
Non Coding Rnas ◽  
Alamarblue Assay

Triptolide is a diterpene triepoxide, which performs its biological activities via mechanisms including induction of apoptosis, targeting of pro-inflammatory cytokines, and reshaping of the epigenetic landscape of target cells. However, the targeting of long non-coding RNAs (lncRNAs) by triptolide has not yet been investigated, despite their emerging roles as key epigenetic regulators of inflammation and immune cell function during Mycobacterium tuberculosis (Mtb) infection. Hence, we investigated whether triptolide targets inflammation-associated lncRNA-PACER and lincRNA-p21 and how this targeting associates with Mtb killing within monocyte-derived macrophages (MDMs).Using RT-qPCR, we found that triptolide induced the expression of lincRNA-p21 but inhibited the expression of lncRNA-PACER in resting MDMs in a dose- and time-dependent manner. Moreover, Mtb infection induced the expression of lincRNA-p21 and lncRNA-PACER, and exposure to triptolide before or after Mtb infection led to further increase of Mtb-induced expression of these lncRNAs in MDMs. We further found that contrary to lncRNA-PACER, triptolide time- and dose-dependently upregulated Ptgs-2, which is a proximal gene regulated by lncRNA-PACER. Also, low-concentration triptolide inhibited the expression of cytokine IL-6, a known target of lincRNA-p21. Mtb infection induced the expression of IL-6 and Ptgs-2, and triptolide treatment further increased IL-6 but decreased Ptgs-2 expression in Mtb-infected MDMs. The inverse relation between the expression of these lncRNAs and their target genes is concordant with the conception that these lncRNAs mediate, at least partially, the cytotoxic and/or anti-inflammatory activities of triptolide in both resting and activated MDMs. Using the CFU count method, we found that triptolide decreased the intracellular growth of Mtb HN878. The alamarBlue assay showed that this decreased Mtb HN878 growth was not as a result of direct targeting of Mtb HN878 by triptolide, but rather evoking MDMs’ intracellular killing mechanisms which we speculate could include triptolide-induced enhancement of MDMs’ effector killing functions mediated by lncRNA-PACER and lincRNA-p21. Altogether, these results provide proof of the modulation of lncRNA-PACER and lincRNA-p21 expression by triptolide, and a possible link between these lncRNAs, the enhancement of MDMs’ effector killing functions and the intracellular Mtb-killing activities of triptolide. These findings prompt for further investigation of the precise contribution of these lncRNAs to triptolide-induced activities in MDMs.

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