Abstract:
:Rapid reconstruction of genome-scale protein-protein interaction (PPI) networks is instrumental in understanding the cellular processes and disease pathogenesis and drug reactions. However, lack of experimentally verified negative data (i.e., pairs of proteins that do not interact) is still a major issue that needs to be properly addressed in computational modeling. In this study, we take advantage of the very limited experimentally verified negative data from Negatome to infer more negative data for computational modeling. We assume that the paralogs or orthologs of two non-interacting proteins also do not interact with high probability. We coin an assumption as "Neglog" this assumption is to some extent supported by paralogous/orthologous structure conservation. To reduce the risk of bias toward the negative data from Negatome, we combine Neglog with less biased random sampling according to a certain ratio to construct training data. L2-regularized logistic regression is used as the base classifier to counteract noise and train on a large dataset. Computational results show that the proposed Neglog method outperforms pure random sampling method with sound biological interpretability. In addition, we find that independent test on negative data is indispensable for bias control, which is usually neglected by existing studies. Lastly, we use the Neglog method to validate the PPIs in STRING, which are supported by gene ontology (GO) enrichment analyses.
journal_name
Int J Mol Scijournal_title
International journal of molecular sciencesauthors
Mei S,Zhang Kdoi
10.3390/ijms20205075subject
Has Abstractpub_date
2019-10-12 00:00:00issue
20issn
1422-0067pii
ijms20205075journal_volume
20pub_type
杂志文章abstract::Antimicrobial lipids such as fatty acids and monoglycerides are promising antibacterial agents that destabilize bacterial cell membranes, causing a wide range of direct and indirect inhibitory effects. The goal of this review is to introduce the latest experimental approaches for characterizing how antimicrobial lipid...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms19041114
更新日期:2018-04-08 00:00:00
abstract::The ghrelin system has received substantial recognition as a potential target for novel anti-seizure drugs. Ghrelin receptor (ghrelin-R) signaling is complex, involving Gαq/11, Gαi/o, Gα12/13, and β-arrestin pathways. In this study, we aimed to deepen our understanding regarding signaling pathways downstream the ghrel...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms20102480
更新日期:2019-05-20 00:00:00
abstract::Human cytomegalovirus (HCMV) is ubiquitously prevalent. HCMV infection is typically asymptomatic and controlled by the immune system in healthy individuals, yet HCMV can be severely pathogenic for the fetus during pregnancy and in immunocompromised persons, such as transplant recipients or HIV infected patients. HCMV ...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms20153626
更新日期:2019-07-24 00:00:00
abstract::Present day awareness of biofilm colonization on polymeric surfaces has prompted the scientific community to develop an ever-increasing number of new materials with anti-biofilm features. However, compared to the large amount of work put into discovering potent biofilm inhibitors, only a small number of papers deal wi...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms20153794
更新日期:2019-08-03 00:00:00
abstract::Humans are exposed to phthalates released from plastics, cosmetics, or food on a daily basis. Phthalates have low acute liver toxicity, but their chronic exposures could induce molecular and cellular effects linked to adverse health outcomes, such as liver tumor promotion or chronic liver diseases. The alternation of ...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms21176069
更新日期:2020-08-23 00:00:00
abstract::Hepatocellular carcinoma (HCC) is a leading cause of cancer-related morbidity and mortality worldwide. Most patients are diagnosed with advanced disease, limiting their options for treatment. While current treatments are adequate for lower staged disease, available systemic treatments are limited, with marginal benefi...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms21186757
更新日期:2020-09-15 00:00:00
abstract::The involvement of microRNAs in the control of repressors of human γ-globin gene transcription has been firmly demonstrated, as described for the miR-486-3p mediated down-regulation of BCL11A. On the other hand, we have reported that miR-210 is involved in erythroid differentiation and, possibly, in γ-globin gene up-r...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms18122530
更新日期:2017-11-26 00:00:00
abstract::Sex reversal has been used as a breeding strategy by salmonid fish to produce genetically and phenotypically single sex populations. Production of all-female fish has great importance for the creation of monosex female triploids of salmonid fish, which are valued for their sterility, lack of female maturation, and lar...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms22020964
更新日期:2021-01-19 00:00:00
abstract::Abiotic stresses are major constraints limiting crop growth and production. Heat shock factors (Hsfs) play significant roles in mediating plant resistance to various environmental stresses, including heat, drought and salinity. In this study, we explored the biological functions and underlying mechanisms of wheat TaHs...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms21093121
更新日期:2020-04-28 00:00:00
abstract::Near infrared fluorescence (NIRF) imaging has strong potential for widespread use in noninvasive tumor imaging. Indocyanine green (ICG) is the only Food and Drug Administration (FDA) -approved NIRF dye for clinical diagnosis; however, it is unstable and poorly targets tumors. DZ-1 is a novel heptamethine cyanine NIRF ...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms18061332
更新日期:2017-06-21 00:00:00
abstract::Ovarian granulosa cells (GCs) are a critical approach to investigate the mechanism of gene regulation during folliculogenesis. The objective of this study was to investigate the role of MT2 in bovine GCs, and assess whether MT2 silencing affected GCs response to melatonin. We found that MT2 silencing significantly dec...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms19072028
更新日期:2018-07-12 00:00:00
abstract::Major depressive disorder (MDD) represents a serious health problem estimated to affect 350 million people globally. Importantly, MDD has repeatedly emerged as an etiological or prognostic factor in cardiovascular disease (CVD) development, including vascular pathology. Several linking pathomechanisms between MDD and ...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms21072317
更新日期:2020-03-27 00:00:00
abstract::Due to the addressability and programmability, DNA has been applied not merely in constructing static elegant nanostructures such as two dimensional and three dimensional DNA nanostructures but also in designing dynamic nanodevices. Moreover, DNA could combine with hydrophobic organic molecules to be a new amphiphilic...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms19082283
更新日期:2018-08-03 00:00:00
abstract::Neural diseases including injury by endogenous factors, traumatic brain injury, and degenerative neural injury are eventually due to reactive oxygen species (ROS). Thus ROS generation in neural tissues is a hallmark feature of numerous forms of neural diseases. Neural degeneration and the neural damage process is comp...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms160819657
更新日期:2015-08-19 00:00:00
abstract::In the last decade, a wide range of avian influenza viruses (AIVs) have infected various mammalian hosts and continuously threaten both human and animal health. It is a result of overcoming the inter-species barrier which is mostly associated with gene reassortment and accumulation of mutations in their gene segments....
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms18122706
更新日期:2017-12-13 00:00:00
abstract::The bromodomain and extra-terminal domain family inhibitors (BETi) are a promising new class of anticancer agents. Since numerous anticancer drugs have been correlated to cardiomyopathy, and since BETi can affect non-cancerous tissues, we aimed to investigate in healthy animals any ultrastructural BETi-induced alterat...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms20071527
更新日期:2019-03-27 00:00:00
abstract::Neoplastic growth and cellular differentiation are critical hallmarks of tumor development. It is well established that cell-to-cell communication between tumor cells and "normal" surrounding cells regulates tumor differentiation and proliferation, aggressiveness, and resistance to treatment. Nevertheless, the mechani...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms19051270
更新日期:2018-04-24 00:00:00
abstract::Lysozyme is widely used as a model protein in studies of structure-function relationships. Recently, lysozyme has gained attention for use in accelerating the degradation of secondary sludge, which mainly consists of bacteria. However, a high-throughput screening system for lysozyme engineering has not been reported. ...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms21228668
更新日期:2020-11-17 00:00:00
abstract::Chitin synthase synthesizes chitin, which is critical for the arthropod exoskeleton. In this study, we cloned the cDNA sequences of a chitin synthase 1 gene, PcCHS1, in the citrus red mite, Panonychus citri (McGregor), which is one of the most economically important pests of citrus worldwide. The full-length cDNA of P...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms15033711
更新日期:2014-02-28 00:00:00
abstract::The emergence of the novel coronavirus in Wuhan, China, which causes severe respiratory tract infections in humans (COVID-19), has become a global health concern. Most coronaviruses infect animals but can evolve into strains that cross the species barrier and infect humans. At the present, there is no single specific ...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms21072272
更新日期:2020-03-25 00:00:00
abstract::Various strategies have been employed to speed tissue regeneration using bioactive molecules. Interestingly, platelet concentrates derived from a patient's own blood have been utilized as a regenerative strategy in recent years. In the present study, a novel liquid platelet formulation prepared without the use of anti...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms18020331
更新日期:2017-02-04 00:00:00
abstract::Metabolic reprogramming that favors high glycolytic flux with lactate production in normoxia is among cancer hallmarks. Lactate is an essential oncometabolite regulating cellular redox homeostasis, energy substrate partitioning, and intracellular signaling. Moreover, malignant phenotype's chief characteristics are dep...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms21249676
更新日期:2020-12-18 00:00:00
abstract::The frequency and volume of Asian sand dust (ASD) (Kosa) are increasing in Japan, and it has been reported that ASD may cause adverse respiratory effects. The pulmonary toxicity of ASD has been previously analyzed in mice exposed to ASD particles by intratracheal instillation. To study the pulmonary toxicity induced b...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms19020416
更新日期:2018-01-31 00:00:00
abstract::The mushroom Inonotus obliquus has been widely used as a folk medicine in Russia, Poland and most of the Baltic countries. In this study, water-soluble and alkali-soluble crude polysaccharides (IOW and IOA) were isolated from I. obliquus, and the carbohydrate-rich fractions IOW-1 and IOA-1 were obtained respectively a...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms13079194
更新日期:2012-01-01 00:00:00
abstract::Uterine fibroids (UFs) are the most common tumors of the female genital tract. The effect of UFs on the quality of life and the overall cost of treatment are significant issues worldwide. Tumor size and location are the two specific factors which influence the occurrence of symptoms, the need for, and method of, treat...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms18122586
更新日期:2017-12-01 00:00:00
abstract::The insulin/insulin-like growth factor (IGF) system in mammals comprises a dynamic network of proteins that modulate several biological processes such as development, cell growth, metabolism, and aging. Dysregulation of the insulin/IGF system has major implications for several pathological conditions such as diabetes ...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms18091921
更新日期:2017-09-07 00:00:00
abstract::Trials using antisense oligonucleotide technology to lower Huntingtin levels in Huntington's disease (HD) are currently ongoing. This progress, taking place only 27 years after the identification of the Huntingtin gene (HTT) in 1993 reflects the enormous development in genetic engineering in the last decades. It is al...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms21062146
更新日期:2020-03-20 00:00:00
abstract::Lung cancer is the leading cause of cancer deaths worldwide. Therefore, for the prevention, diagnosis, prognosis and treatment of lung cancer, efficient preventive strategies and new therapeutic strategies are needed to face these challenges. Natural bioactive compounds and particular flavonoids compounds have been pr...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms20174291
更新日期:2019-09-02 00:00:00
abstract::Doxorubicin (DOX) is an anthracycline drug with a wide spectrum of antineoplastic activities. However, it causes cardiac cytotoxicity, and this limits its clinical applications. MicroRNA-21 (miR-21) plays a vital role in regulating cell proliferation and apoptosis. While miR-21 is preferentially expressed in adult car...
journal_title:International journal of molecular sciences
pub_type: 杂志文章
doi:10.3390/ijms160714511
更新日期:2015-06-26 00:00:00
abstract::Derivatives of 3,4-hydroxypyridinones have been extensively studied for in vivo Fe3+ sequestration. Deferiprone, a 1,2-dimethyl-3,4-hydroxypyridinone, is now routinely used for clinical treatment of iron overload disease. Hexadentate tris(3,4-hydroxypyridinone) ligands (THP) complex Fe3+ at very low iron concentration...
journal_title:International journal of molecular sciences
pub_type: 杂志文章,评审
doi:10.3390/ijms18010116
更新日期:2017-01-08 00:00:00