Abstract：
:Accurate identification of protein-protein interactions (PPI) is the key step in understanding proteins' biological functions, which are typically context-dependent. Many existing PPI predictors rely on aggregated features from protein sequences, however only a few methods exploit local information about specific residue contacts. In this work we present a two-stage machine learning approach for prediction of protein-protein interactions. We start with the carefully filtered data on protein complexes available for Saccharomyces cerevisiae in the Protein Data Bank (PDB) database. First, we build linear descriptions of interacting and non-interacting sequence segment pairs based on their inter-residue distances. Secondly, we train machine learning classifiers to predict binary segment interactions for any two short sequence fragments. The final prediction of the protein-protein interaction is done using the 2D matrix representation of all-against-all possible interacting sequence segments of both analysed proteins. The level-I predictor achieves 0.88 AUC for micro-scale, i.e., residue-level prediction. The level-II predictor improves the results further by a more complex learning paradigm. We perform 30-fold macro-scale, i.e., protein-level cross-validation experiment. The level-II predictor using PSIPRED-predicted secondary structure reaches 0.70 precision, 0.68 recall, and 0.70 AUC, whereas other popular methods provide results below 0.6 threshold (recall, precision, AUC). Our results demonstrate that multi-scale sequence features aggregation procedure is able to improve the machine learning results by more than 10% as compared to other sequence representations. Prepared datasets and source code for our experimental pipeline are freely available for download from: http://zubekj.github.io/mlppi/ (open source Python implementation, OS independent).
journal_name
PeerJjournal_title
PeerJauthors
Zubek J,Tatjewski M,Boniecki A,Mnich M,Basu S,Plewczynski Ddoi
10.7717/peerj.1041subject
Has Abstractpub_date
2015-07-02 00:00:00pages
e1041issn
2167-8359pii
1041journal_volume
3pub_type
杂志文章相关文献
PeerJ文献大全abstract：Background:Hair follicles in cashmere goats are divided into primary and secondary hair follicles (HFs). HF development, which determines the morphological structure, is regulated by a large number of vital genes; however, the key functional genes and their interaction networks are still unclear. Although the vitamin D...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7230
更新日期：2019-07-03 00:00:00
abstract：BACKGROUND:The Saururaceae, a very small family of Piperales comprising only six species in four genera, have a relatively scanty fossil record outside of Europe. The phylogenetic relationships of the four genera to each other are resolved, with the type genus Saururus occurring in both eastern North America and East A...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.3434
更新日期：2017-06-13 00:00:00
abstract：:Dorsal horn neurons in the spinal cord integrate and relay sensory information to higher brain centers. These neurons are organized in specific laminae and different transcription factors are involved in their specification. The murine homeodomain Gbx1 protein is expressed in the mantle zone of the spinal cord at E12....
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.142
更新日期：2013-08-29 00:00:00
abstract：:Vitellogenin has been proposed to regulate division of labor and social organization in social insects. The red imported fire ant (Solenopsis invicta) harbors four distinct, adjacent vitellogenin genes (Vg1, Vg2, Vg3, and Vg4). Contrary to honey bees that have a single Vg ortholog as well as potentially fertile nurses...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.4875
更新日期：2018-05-28 00:00:00
abstract：:The use of baited remote underwater video (BRUV) for examining and monitoring marine biodiversity in temperate marine environments is rapidly growing, however many aspects of their effectiveness relies on assumptions based on studies from the Southern Hemisphere. The addition of bait to underwater camera systems acts ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.9744
更新日期：2020-08-27 00:00:00
abstract：:Alzheimer's disease is a multifactorial disorder caused by the interaction of genetic, epigenetic and environmental factors. The formation of cytotoxic oligomers consisting of Aβ peptide is widely accepted as being one of the main key events triggering the development of Alzheimer's disease. Aβ peptide production resu...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.3086
更新日期：2017-04-12 00:00:00
abstract：Background:Low-carbohydrate, high-fat (LCHF) diets are useful for treating a range of health conditions, but there is little research evaluating the degree of carbohydrate restriction on outcome measures. This study compares anthropometric and cardiometabolic outcomes between differing carbohydrate-restricted diets. O...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.6273
更新日期：2019-02-05 00:00:00
abstract：Introduction:Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded on the mapping of sequencing reads onto known genomic r...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.6174
更新日期：2019-01-30 00:00:00
abstract：:Transmissible gastroenteritis virus (TGEV), belonging to the coronaviridae family, is the key cause of the fatal diarrhea of piglets and results in many pathological processes. microRNAs (miRNAs) play a key role in the regulation of virus-induced apoptosis. During the process of apoptosis induced by TGEV infection in ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1635
更新日期：2016-02-04 00:00:00
abstract：Background:Chloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could c...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7558
更新日期：2019-09-24 00:00:00
abstract：:Resistance strategies of clonal organs, and parent and offspring shoots of Phragmites australis (common reed) to heavy metal pollution in soils are not well known. To clarify the tolerance or resistance strategies in reeds, we conducted a pot experiment with five levels of Pb concentration (0∼4,500 mg kg-1) in flood a...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.4188
更新日期：2018-01-03 00:00:00
abstract：:The Eocene history of cetacean evolution is now represented by the expansive fossil record of archaeocetes elucidating major morphofunctional shifts relating to the land to sea transition, but the change from archaeocetes to modern cetaceans is poorly established. New fossil material of the recently recognized family ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1129
更新日期：2015-09-10 00:00:00
abstract：:Bone microstructure has long been known as a powerful tool to investigate lifestyle-related biomechanical constraints, and many studies have focused on identifying such constraints in the limb bones of aquatic or arboreal mammals in recent years. The limb bone microstructure of fossorial mammals, however, has not been...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.5216
更新日期：2018-07-11 00:00:00
abstract：Background:WRKY proteins play a vital role in the plants response to different stresses, growth and development. Studies of WRKY proteins have been mainly focused on model plant Arabidopsis and a few other vegetable plants. However, the systematical study of eggplant WRKY transcription factor superfamily is scarce. Me...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.8777
更新日期：2020-03-17 00:00:00
abstract：:The structural complexity of coral reefs plays a major role in the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional metrics with 2-dimensional properties are inadequate for characterization of reef structural complexity. A 3-dimensional (3D) approach can better quantify topography...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1077
更新日期：2015-07-07 00:00:00
abstract：:The incorporation of feedback into a person's body schema is well established. The crossmodal congruency task (CCT) is used to objectively quantify incorporation without being susceptible to experimenter biases. This visual-tactile interference task is used to calculate the crossmodal congruency effect (CCE) score as ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.6976
更新日期：2019-05-22 00:00:00
abstract：:Ocean warming threatens the functioning of coral reef ecosystems by inducing mass coral bleaching and mortality events. The link between temperature and coral bleaching is now well-established based on observations that mass bleaching events usually occur when seawater temperatures are anomalously high. However, times...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7473
更新日期：2019-08-12 00:00:00
abstract：:The Asian clam, Corbicula fluminea, is a commonly consumed small freshwater bivalve in East Asia. However, available genetic information of this clam is still limited. In this study, the transcriptome of female C. fluminea was sequenced using the Illumina HiSeq 2500 platform. A total of 89,563 unigenes were assembled ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7770
更新日期：2019-10-22 00:00:00
abstract：:Palythoa caribaeorum is a zoanthid often dominant in shallow rocky environments along the west coast of the Atlantic Ocean, from the tropics to the subtropics. This species has high environmental tolerance and is a good space competitor in reef environments. Considering current and future scenarios in the global clima...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.4777
更新日期：2018-05-17 00:00:00
abstract：Background:As the most frequently occurred tumor in biliary tract, cholangiocarcinoma (CCA) is mainly characterized by its late diagnosis and poor outcome. It is therefore urgent to identify specific genes and pathways associated with its progression and prognosis. Materials and Methods:The differentially expressed ge...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7968
更新日期：2019-10-31 00:00:00
abstract：:Hydrolysis of ATP by Na+/K+-ATPase, a P-Type ATPase, catalyzing active Na+ and K+ transport through cellular membranes leads transiently to a phosphorylation of its catalytical α-subunit. Surprisingly, three-dimensional molecular structure analysis of P-type ATPases reveals that binding of ATP to the N-domain connecte...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.3087
更新日期：2017-03-14 00:00:00
abstract：BACKGROUND:Constant reviews of the caring behavior of nurses and patient satisfaction help to improve the quality of nursing. The aim of our research was to explore relationships between the level of nursing education, the perception of nurses and nursing assistants of Watson's carative factors, and patient satisfactio...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.2940
更新日期：2017-02-07 00:00:00
abstract：Background:G. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released durin...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.8065
更新日期：2019-12-18 00:00:00
abstract：:The currently-accepted dogma when analysing human Alu transposable elements is that 'young' Alu elements are found in low GC regions and 'old' Alus in high GC regions. The correlation between high GC regions and high gene frequency regions make this observation particularly difficult to explain. Although a number of s...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.78
更新日期：2013-05-21 00:00:00
abstract：:Background.Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.2097
更新日期：2016-06-07 00:00:00
abstract：:Inherent difficulties of tracking and observing organisms in the field often leave researchers with no choice but to conduct behavioral experiments under laboratory settings. However, results of laboratory experiments do not always translate accurately to natural conditions. A fundamental challenge in ecology is there...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1918
更新日期：2016-04-11 00:00:00
abstract：:This study aimed to characterize the antioxidant properties of Rama Forte persimmon, a tannin-rich fruit variety produced in Brazil. Extracts prepared with lyophilized pulps from fruits obtained in local markets were analyzed individually to evaluate the extent of antioxidant protection and investigate the antioxidant...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.5223
更新日期：2018-07-25 00:00:00
abstract：:Flatfish undergo extreme morphological development and settle to a benthic in the adult stage, and are likely to be more susceptible to environmental stress. Heat shock proteins 70 (hsp70) are involved in embryonic development and stress response in metazoan animals. However, the evolutionary history and functions of ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7781
更新日期：2019-11-11 00:00:00
abstract：Introduction:A high body fat coupled with low cardiopulmonary fitness and an increase in oxidative stress has been connoted as contributing factors in developing cardiovascular comorbidities. This study aimed to investigate the correlation between antioxidants and oxidative stress status with cardiopulmonary responses ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.9230
更新日期：2020-05-19 00:00:00
abstract：:Increasing cross-border trade of medicinal and aromatic plants (MAPs) has put heavy pressure on a considerable number of species in the Himalayas. One of the threatened species in Nepal is Aconitum spicatum. Unfortunately for this species and for many others, our knowledge on population ecology and performance across ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7574
更新日期：2019-09-10 00:00:00
