Dataset Information

HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.

ABSTRACT: HitPredict is a consolidated resource of experimentally identified, physical protein-protein interactions with confidence scores to indicate their reliability. The study of genes and their inter-relationships using methods such as network and pathway analysis requires high quality protein-protein interaction information. Extracting reliable interactions from most of the existing databases is challenging because they either contain only a subset of the available interactions, or a mixture of physical, genetic and predicted interactions. Automated integration of interactions is further complicated by varying levels of accuracy of database content and lack of adherence to standard formats. To address these issues, the latest version of HitPredict provides a manually curated dataset of 398 696 physical associations between 70 808 proteins from 105 species. Manual confirmation was used to resolve all issues encountered during data integration. For improved reliability assessment, this version combines a new score derived from the experimental information of the interactions with the original score based on the features of the interacting proteins. The combined interaction score performs better than either of the individual scores in HitPredict as well as the reliability score of another similar database. HitPredict provides a web interface to search proteins and visualize their interactions, and the data can be downloaded for offline analysis. Data usability has been enhanced by mapping protein identifiers across multiple reference databases. Thus, the latest version of HitPredict provides a significantly larger, more reliable and usable dataset of protein-protein interactions from several species for the study of gene groups. Database URL: http://hintdb.hgc.jp/htp.

SUBMITTER: Lopez Y

PROVIDER: S-EPMC4691340 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.

López Yosvany Y Nakai Kenta K Patil Ashwini A

Database : the journal of biological databases and curation 20151226

HitPredict is a consolidated resource of experimentally identified, physical protein-protein interactions with confidence scores to indicate their reliability. The study of genes and their inter-relationships using methods such as network and pathway analysis requires high quality protein-protein interaction information. Extracting reliable interactions from most of the existing databases is challenging because they either contain only a subset of the available interactions, or a mixture of phys ...[more]

PMID: 26708988

Similar Datasets

Project description:Experimental high-throughput studies of protein-protein interactions are beginning to provide enough data for comprehensive computational studies. Today, about ten large data sets, each with thousands of interacting pairs, coarsely sample the interactions in fly, human, worm, and yeast. Another about 55,000 pairs of interacting proteins have been identified by more careful, detailed biochemical experiments. Most interactions are experimentally observed in prokaryotes and simple eukaryotes; very few interactions are observed in higher eukaryotes such as mammals. It is commonly assumed that pathways in mammals can be inferred through homology to model organisms, e.g. the experimental observation that two yeast proteins interact is transferred to infer that the two corresponding proteins in human also interact. Two pairs for which the interaction is conserved are often described as interologs. The goal of this investigation was a large-scale comprehensive analysis of such inferences, i.e. of the evolutionary conservation of interologs. Here, we introduced a novel score for measuring the overlap between protein-protein interaction data sets. This measure appeared to reflect the overall quality of the data and was the basis for our two surprising results from our large-scale analysis. Firstly, homology-based inferences of physical protein-protein interactions appeared far less successful than expected. In fact, such inferences were accurate only for extremely high levels of sequence similarity. Secondly, and most surprisingly, the identification of interacting partners through sequence similarity was significantly more reliable for protein pairs within the same organism than for pairs between species. Our analysis underlined that the discrepancies between different datasets are large, even when using the same type of experiment on the same organism. This reality considerably constrains the power of homology-based transfer of interactions. In particular, the experimental probing of interactions in distant model organisms has to be undertaken with some caution. More comprehensive images of protein-protein networks will require the combination of many high-throughput methods, including in silico inferences and predictions. http://www.rostlab.org/results/2006/ppi_homology/

Project description:BackgroundThe International Physical Actvity Questionnaire (IPAQ) is a validated tool for physical activity assessment used in many countries however no Arabic version of the long-form of this questionnaire exists to this date. Hence, the aim of this study was to cross-culturally adapt and validate an Arabic version of the long International Physical Activity Questionnaire (AIPAQ) equivalent to the French version (F-IPAQ) in a Lebanese population.MethodsThe guidelines for cross-cultural adaptation provided by the World Health Organization and the International Physical Activity Questionnaire committee were followed. One hundred fifty-nine students and staff members from Saint Joseph University of Beirut were randomly recruited to participate in the study. Items of the A-IPAQ were compared to those from the F-IPAQ for concurrent validity using Spearman's correlation coefficient. Content validity of the questionnaire was assessed using factor analysis for the A-IPAQ's items. The physical activity indicators derived from the A-IPAQ were compared with the body mass index (BMI) of the participants for construct validity. The instrument was also evaluated for internal consistency reliability using Cronbach's alpha and Intraclass Correlation Coefficient (ICC). Finally, thirty-one participants were asked to complete the A-IPAQ on two occasions three weeks apart to examine its test-retest reliability. Bland-Altman analyses were performed to evaluate the extent of agreement between the two versions of the questionnaire and its repeated administrations.ResultsA high correlation was observed between answers of the F-IPAQ and those of the A-IPAQ, with Spearman's correlation coefficients ranging from 0.91 to 1.00 (p < 0.05). Bland-Altman analysis showed a high level of agreement between the two versions with all values scattered around the mean for total physical activity (mean difference = 5.3 min/week, 95% limits of agreement = -145.2 to 155.8). Negative correlations were observed between MET values and BMI, independent of age, gender or university campus. The A-IPAQ showed a high internal consistency reliability with Cronbach's alpha ranging from 0.769-1.00 (p < 0.001) and intraclass correlation coefficient (ICC) ranging from 0.625-0.999 (p < 0.001), except for a moderate agreement with the moderate garden/yard activity (alpha = 0.682; ICC = 0.518; p < 0.001). The A-IPAQ had moderate-to-good test-retest reliability for most of its items (ICC ranging from 0.66-0.96; p < 0.001) and the Bland-Altman analysis showed a satisfactory agreement between the two administrations of the A-IPAQ for total physical activity (mean difference = 99.8 min/week, 95% limits of agreement = -1105.3; 1304.9) and total vigorous and moderate physical activity (mean difference = -29.7 min/week, 95% limits of agreement = -777.6; 718.2).ConclusionThe modified Arabic version of the IPAQ showed acceptable validity and reliability for the assessment of physical activity among Lebanese adults. More studies are necessary in the future to assess its validity compared to a gold-standard criterion measure.

Project description:BackgroundThis study aimed to determine the validity of the Malay-translated version scales for assessing the social support and physical environment for exercise activities.MethodThe study was a cross-sectional design in nature, using self-reported questionnaires among the university students in Malaysia. Participants were selected using a convenience sampling approach. Perceptions regarding social support and physical environment were assessed using the Malay-translated version scales. The standard forward-backwards translation was conducted to translate the English version of the scales to the Malay version. Confirmatory factor analysis (CFA) was used to validate the translated version scales; composite reliability (CR) and average variance extracted (AVE) were computed.ResultsA total of 857 students participated in this study (female: 49.1%, male: 50.9%). The mean age of the participants was 20.2 (SD = 1.6). The fit indices of the initial hypothesized measurement models (social support and physical environment) were not satisfactory. Further improvements were made by adding covariances between residuals' items within the same factor for each hypothesized model. The final re-specified measurement models demonstrated adequate factor structure for the social support scale with 24 items (CFI = .932, TLI = .920, SRMR = .054, RMSEA = .061), and the physical environment scale with five items (CFI = .994, TLI = .981, SRMR = .013, RMSEA = .054). The CR was .918 for family support, .919 for friend support, .813 for perceived availability, and .771 for perceived quality. The AVEs were .560 for family support, .547 for friend support, .554 for perceived availability, and .628 for perceived quality. The intra-class correlation (ICC) based on test-retest was .920 for family support, .984 for friend support, .895 for availability of facilities, and .774 for quality of facilities.ConclusionThe Malay version of the social support scale for exercise and the physical environment scale for physical activity were shown to have adequate psychometric properties for assessing perceived social support and physical environment among the university students in Malaysia.PerspectiveThis study presented the psychometric properties of the social support and physical environment scales based on CFA and was the first to translate these scales from the original English version to the Malay version.

Project description:BackgroundAchievement emotions have a significant impact on both the learning process and outcomes. However, there is currently no brief and effective questionnaire available to evaluate Chinese university students' achievement emotions in physical education courses. This study aimed to examine the reliability and validity of the Achievement Emotions for Physical Education Questionnaire (AEQ-PE) in a sample of Chinese university students, while also investigating its measurement invariance across gender and grade levels.MethodsA cluster randomization sampling method was used to select 694 first- and second-year university students in Shanghai, China for the survey. Descriptive statistics, item analysis, reliability testing, and measurement invariance testing were conducted on the full sample (n = 694). Subsequently, the full sample was randomly divided into two groups, with Sample 1 (n = 347) undergoing exploratory factor analysis (EFA), and Sample 2 (n = 347) undergoing confirmatory factor analysis (CFA) to test the structural validity, convergent validity, and discriminant validity of the Chinese version of the Achievement Emotions Questionnaire for Physical Education (AEQ-PE-C). Finally, Sample 3 (n = 45), which was retested one month later, was used to evaluate test-retest reliability.ResultsThe Chinese version of the Achievement Emotions Questionnaire for Physical Education consists of 6 dimensions and 24 items, with good item discrimination. The EFA supported a 6-factor structure model, while the CFA demonstrated good model fit indices (χ2/df = 3.086, CFI = 0.928, TLI = 0.916, RMSEA = 0.078) and good convergent and discriminant validity. The questionnaire exhibits high internal consistency reliability (0.794) and excellent test-retest reliability (0.792). Furthermore, the multi-group analysis confirms that the AEQ-PE-C questionnaire has measurement invariance across gender and grade levels.ConclusionThe Chinese version of the Achievement Emotions Questionnaire for Physical Education has good reliability and validity, as well as measurement invariance across gender and grade levels, making it an effective tool for measuring achievement emotions in physical education among Chinese university students.

Project description:BACKGROUND: Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual curation is intensive in terms of time and cost, there is an urgent need for text-mining tools to facilitate the extraction of such information. The BioCreative (Critical Assessment of Information Extraction systems in Biology) challenge evaluation provided common standards and shared evaluation criteria to enable comparisons among different approaches. RESULTS: During the benchmark evaluation of BioCreative 2006, all of our results ranked in the top three places. In the task of filtering articles irrelevant to physical protein interactions, our method contributes a precision of 75.07%, a recall of 81.07%, and an AUC (area under the receiver operating characteristic curve) of 0.847. In the task of identifying protein mentions and normalizing mentions to molecule identifiers, our method is competitive among runs submitted, with a precision of 34.83%, a recall of 24.10%, and an F1 score of 28.5%. In extracting protein interaction pairs, our profile-based method was competitive on the SwissProt-only subset (precision = 36.95%, recall = 32.68%, and F1 score = 30.40%) and on the entire dataset (30.96%, 29.35%, and 26.20%, respectively). From the biologist's point of view, however, these findings are far from satisfactory. The error analysis presented in this report provides insight into how performance could be improved: three-quarters of false negatives were due to protein normalization problems (532/698), and about one-quarter were due to problems with correctly extracting interactions for this system. CONCLUSION: We present a text-mining framework to extract physical protein-protein interactions from the literature. Three key issues are addressed, namely filtering irrelevant articles, identifying protein names and normalizing them to molecule identifiers, and extracting protein-protein interactions. Our system is among the top three performers in the benchmark evaluation of BioCreative 2006. The tool will be helpful for manual interaction curation and can greatly facilitate the process of extracting protein-protein interactions.

Dataset Information

HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.

Publications

HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets