Systematic comparison of the protein-protein interaction databases from a user's perspective

Publication date: Available online 28 January 2020Source: Journal of Biomedical InformaticsAuthor(s): Akhilesh Kumar Bajpai, Sravanthi Davuluri, Kriti Tiwary, Sithalechumi Narayanan, Sailaja Oguru, Kavyashree Basavaraju, Deena Dayalan, Kavitha Thirumurugan, Kshitish K. AcharyaAbstractIn absence of periodic systematic comparisons, biologists/bioinformaticians may be forced to make a subjective selection among the many protein-protein interaction (PPI) databases and tools. We conducted a comprehensive compilation and comparison of such resources. We compiled 375 PPI resources, short-listed 125 important ones (both lists are available at startbioinfo.com), and compared the features and coverage of 16 carefully-selected databases related to human PPIs. We quantitatively compared the coverage of 'experimentally verified' as well as 'total' (experimentally verified as well as predicted) PPIs for these 16 databases. Coverage was compared in two ways: (a) PPIs obtained in response to gene queries using the web interfaces were compared. As a query set, 108 genes expressed differently across tissues (specific to kidney, testis, and uterus, and ubiquitous - i.e., expressed in 43 human normal tissues) or associated with certain diseases (breast cancer, lung cancer, Alzheimer’s, cystic fibrosis, diabetes, and cardiomyopathy) were chosen. The coverage was also compared for the well-studied genes versus the less-studied ones. The coverage of the databases for high-quality interactions...
Source: Journal of Biomedical Informatics - Category: Information Technology Source Type: research

Related Links:

Publication date: April 2020Source: Phytochemistry Letters, Volume 36Author(s): Fahd M. Abdelkarem, Ezz-Eldin K. Desoky, Alaa M. Nafady, Ahmed E. Allam, Aldoushy Mahdy, Maki Nagata, Tomofumi Miyamoto, Kuniyoshi ShimizuAbstractFurther chemical study of the crude extract of the soft coral Heteroxenia fuscescens (Fam., Xeniidea), led to isolation of two new sterols, Heterofuscesterols A (1) and B (2), a sterol isolated for the first time from natural sources, 3β,5α,6β-trihydroxyandrosta-17-one (3), along with one new hydroperoxy sesquiterpene, Heterofusceterpene A (4), and one known ceramide (5). Their structu...
Source: Phytochemistry Letters - Category: Chemistry Source Type: research
Publication date: June 2020Source: Microchemical Journal, Volume 155Author(s): Karolina Nowak, Marcin Zawadzki, Tomasz JurekAbstractPostmortem diagnosis of hyperglycaemia is a challenge in forensic medicine. Glycated haemoglobin (HbA1c) is considered one of the markers providing an alternative to postmortem determinations of glucose concentration. On the other hand, glycated albumin (GA) may be determined in cases of difficulty in determining HbA1c.The aim of this study was to implement and evaluate the usefulness of methods enabling determination of HbA1c an GA in postmortem material (HbA1c–peripheral blood, GA&ndas...
Source: Microchemical Journal - Category: Chemistry Source Type: research
Publication date: Available online 21 February 2020Source: Chemical Engineering JournalAuthor(s): Meitong Ou, Chao Pan, Yongkang Yu, Xuan Wang, Yun Zhou, Hanjie Zhang, Qinzhen Cheng, Meiying Wu, Xiaoyuan Ji, Lin MeiAbstractExcessive reactive oxygen species (ROS), as effective cancer therapeutic agents, can promote tumor apoptosis. However, the clinical applications of ROS-mediated cancer therapies still have many limitations, such as self-defects of traditional photosensitizer, adverse tumor microenvironment (TME), and insufficient ROS production. Here, two-dimensional and highly oxidized ilmenite nanosheets (HOIL NSs, for...
Source: Chemical Engineering Journal - Category: Chemistry Source Type: research
Publication date: Available online 21 February 2020Source: Chemical Engineering JournalAuthor(s): Yang Zhang, Yanjun Xu, Di Sun, Zheying Meng, Weiwei Ying, Wei Gao, Rui Hou, Yuanyi Zheng, Xiaojun Cai, Bing Hu, Xianfang LinAbstractAs a promising treatment modality with spatial and temporal control, alternating magnetic field (AMF) triggered magnetic hyperthermal therapy (MHT) shows broad and promising applications to overcome the drawbacks of traditional focal therapies in combating cancer. However, the MHT efficacy is still not satisfactory with the presence of heat shock proteins (HSPs). In addition, sustained tumor hypox...
Source: Chemical Engineering Journal - Category: Chemistry Source Type: research
Chem. Commun., 2020, Accepted Manuscript DOI: 10.1039/D0CC00416B, CommunicationXinwei Tian, Zhao Li, Ning Ding, Jiahang Zhang We have developed a novel near-infrared ratiometric fluorescent theranostic nanoprobe. Reaction with glutathione, it would release a near-infrared fluorophore and chemotherapy drug. Notably, this nanoprobe can selectively kill cancer HeLa,... The content of this RSS Feed (c) The Royal Society of Chemistry
Source: RSC - Chem. Commun. latest articles - Category: Chemistry Authors: Source Type: research
ABSTRACT: Introduction: In high-income countries, persons of high socioeconomic status (SES) have a lower cardiovascular risk. However, in middle and low-income countries, the results are controversial. Objective: To evaluate the association between family income and cardiovascular risk factors in young adults. Methods: A total of 2,063 individuals of a birth cohort initiated in 1978/79 in the city of Ribeir ão Preto, Brazil, were evaluated at age of 23/25 years. Cardiovascular risk factors (hypertension, sedentary lifestyle, smoking, low high-density lipoprotein (HDL)-cholesterol, high low-density lipoprotein (LDL)...
Source: Revista Brasileira de Epidemiologia - Category: Epidemiology Source Type: research
Conclusion: The findings, such as the inverse relationship with tuberculosis treatment discontinuation in the group of people with comorbidity, reinforce the importance of integrated actions in health services to change the scenario of this challenging comorbidity.
Source: Revista Brasileira de Epidemiologia - Category: Epidemiology Source Type: research
This article presents her outstanding character and most important lines of research. The focus of her studies covered alkylative and oxidative damage to DNA bases, in particular mutagenic and carcinogenic properties of purines with an open imidazole ring and 8-oxo-7,8-dihydroguanine (8-oxoGua). They also included analysis of mutagenic properties and pathways for the repair of DNA adducts of lipid peroxidation (LPO) products arising in large quantities during inflammation. Professor Tudek did all of this in the hope of deciphering the mechanisms of DNA damage removal, in particular by the base excision repair (BER) pathway...
Source: Mutation Research Genetic Toxicology and Environmental Mutagenesis - Category: Genetics & Stem Cells Source Type: research
ConclusionsBlood Metallothionein- 2A relative expression and oxidant status may have a prognostic value in breast cancer patients.
Source: Meta Gene - Category: Genetics & Stem Cells Source Type: research
Authors: Gok M, Sozuer E, Topal U, Akyuz M, Bozkurt GK, Hamurcu M, Deniz K Abstract Appendix vermiformis agenesis is quite rare. It is seen in 1/100,000 of patients who underwent laparotomy with an initial diagnosis of appendicitis. A 72-year-old woman who had not undergone any previous surgery was operated on for mechanical intestinal obstruction. Right hemicolectomy was performed due to obstructive tumoral mass in the hepatic flexure. There was no appendix vermiformis in exploration. Before deciding on the diagnosis of appendix agenesis, a thorough and rigorous exploration should be performed in ileocecal region ...
Source: Annali Italiani di Chirurgia - Category: Surgery Tags: Ann Ital Chir Source Type: research
More News: Biology | Breast Cancer | Cancer | Cancer & Oncology | Cancer of the Uterus | Cardiology | Cardiomyopathy | Cystic Fibrosis | Databases & Libraries | Diabetes | Endocrinology | Genetics | Heart | Information Technology | Lung Cancer | Study | Urology & Nephrology