In a differential gene experiment, a cell perturbation can be measured on a microarray before and after the perturbation. The information from these microarrays can then be used to inference genetic pathways and protein-protein interaction networks. In this paper we reverse this idea somewhat and measure a cell perturbation through microarrays and then rely on a protein interaction map to assess which proteins are most likely influenced by the specific perturbation. This in turn helps to elucidate the functional effect the perturbation has on the cell system. The first part of the paper focuses on the propagation model we developed to obtain this information. The second part of the paper reports on a specific experiment that was driven by the interpretation we obtained through such a gene influence network. We applied a PC12 cell line that allows doxocyclin-dependent expression of constitutive active mitogen-activated protein kinase-activated protein kinase (MAPKAPK5 or MK5) to compare the

Within the cell, biosynthetic pathways are embedded in protein-protein interaction networks. In Arabidopsis, the biosynthetic pathways of aliphatic and indole glucosinolate defense compounds are well-characterized. However, little is known about the spatial orchestration of these enzymes and their interplay with the cellular environment. To address these aspects, we applied two complementary, untargeted approaches - split-ubiquitin yeast 2-hybrid and co-immunoprecipitation screens - to identify proteins interacting with CYP83A1 and CYP83B1, two homologous enzymes specific for aliphatic and indole glucosinolate biosynthesis, respectively. Our analyses reveal distinct functional networks with substantial interconnection among the identified interactors for both pathway-specific markers, and add to our knowledge about how biochemical pathways are connected to cellular processes. Specifically, a group of protein interactors involved in cell death and the hypersensitive response provides a potential link

Genetics and biochemistry have been used to map many of the individual pathways that establish and maintain cell polarity in yeast, but Drees et al. (page 549) have now produced the equivalent of an aerial photograph of these processes. Using a high-throughput yeast two-hybrid screen, the authors assayed the universe of likely protein-protein interactions involved in cell polarity development. The resulting protein interaction map provides tantalizing insights and identifies dozens of potential mechanistic connections worth closer examination.. The authors used 68 yeast proteins associated with the actin cytoskeleton, septins, the secretory apparatus, and Rho-type GTPases as baits in parallel two-hybrid screens covering ∼90% of the predicted Saccharomyces cerevisiae ORFs. The screen uncovered 128 novel protein-protein interactions, including 44 involving previously uncharacterized proteins. The appearance of known interactions in the screen, along with subcellular localization studies, ...

TY - JOUR. T1 - Protein interaction networks revealed by proteome coevolution. AU - Cong, Qian. AU - Anishchenko, Ivan. AU - Ovchinnikov, Sergey. AU - Baker, David. N1 - Funding Information: This project has been funded in part with Washington Research Foundation, National Institute of General Medical Sciences (grant no. R01-GM092802-07), National Institute of Allergy and Infectious Diseases (contract no. HHSN272201700059C), and Office of the Director of the National Institutes of Health (grant no. DP5OD026389). This research used resources of the National Energy Research Scientific Computing Center (contract no. DE-AC02-05CH11231).. PY - 2019. Y1 - 2019. N2 - Residue-residue coevolution has been observed across a number of protein-protein interfaces, but the extent of residue coevolution between protein families on the whole-proteome scale has not been systematically studied. We investigate coevolution between 5.4 million pairs of proteins in Escherichia coli and between 3.9 millions pairs in ...

mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate the interactome. menthas approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli ...

Although protein-peptide interactions are estimated to constitute up to 40% of all protein interactions, relatively little information is available for the structural details of these interactions. Peptide-mediated interactions are a prime target for drug design because they are predominantly present in signaling and regulatory networks. A reliable data set of nonredundant protein-peptide complexes is indispensable as a basis for modeling and design, but current data sets for protein-peptide interactions are often biased towards specific types of interactions or are limited to interactions with small ligands. In PepX (http://pepx.switchlab.org), we have designed an unbiased and exhaustive data set of all protein-peptide complexes available in the Protein Data Bank with peptide lengths up to 35 residues. In addition, these complexes have been clustered based on their binding interfaces rather than sequence homology, providing a set of structurally diverse protein-peptide interactions. The final ...

Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. Understanding the mechanisms cells use to accomplish this important process requires a detailed molecular description of the networks involved. We have developed a computational approach for generating static models of signal transduction networks which utilizes protein-interaction maps generated from large-scale two-hybrid screens and expression profiles from DNA microarrays. Networks are determined entirely by integrating protein-protein interaction data with microarray expression data, without prior knowledge of any pathway intermediates. In effect, this is equivalent to extracting subnetworks of the protein interaction dataset whose members have the most correlated expression profiles. We show that our technique accurately reconstructs MAP Kinase signaling networks in Saccharomyces cerevisiae.

virus mentha archives evidence about viral interactions collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. virus mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate the interactome. virus menthas approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. virus mentha offers direct access to viral families such as: Orthomyxoviridae, Orthoretrovirinae and Herpesviridae plus, it offers the unique possibility of searching ...

The primary constituent of the amyloid plaque, beta-amyloid (Abeta), is thought to be the causal toxic moiety of Alzheimers disease. However, despite much work focused on both Abeta and its parent protein, amyloid precursor protein (APP), the functional roles of APP and its cleavage products remain to be fully elucidated. Protein-protein interaction networks can provide insight into protein function, however, high-throughput data often report false positives and are in frequent disagreement with low-throughput experiments. Moreover, the complexity of the CNS is likely to be under represented in such databases. Therefore, we curated the published work characterizing both APP and Abeta to create a protein interaction network of APP and its proteolytic cleavage products, with annotation, where possible, to the level of APP binding domain and isoform. This is the first time that an interactome has been refined to domain level, essential for the interpretation of APP due to the presence of ...

Looking for online definition of Reduced expression in cancer protein in the Medical Dictionary? Reduced expression in cancer protein explanation free. What is Reduced expression in cancer protein? Meaning of Reduced expression in cancer protein medical term. What does Reduced expression in cancer protein mean?

We have mapped SARS CoV-2 human Protein-Protein Interactions from A SARS-CoV-2 protein interaction map reveals targets for drug repurposing human drug target interacted with SARS CoV-2 are highlighted in black arrow. ...

Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins. The fraction of interactions detected in independent screens can be very small, and an outstanding challenge is to determine the reason for the low overlap. Low overlap can arise from either …

CTD curates specific chemical-gene and -protein interactions in vertebrates and invertebrates from published references. You may search for specific types of interactions by selecting a term or terms in this field. Each interaction has a degree and type as defined below. Degree. Each chemical-gene interaction is qualified by a degree: increases, decreases, affects, or does not affect (e.g., Chemical X increases expression of Gene Y mRNA). The affects degree is used when the reference does not describe a more specific degree. Interactions having the does not affect degree are excluded from our public data. An interaction type must be selected in order to filter by degree(s). At least one degree must be checked. Type. To select or deselect multiple interaction types, hold the Ctrl key (PC) or ⌘/Open-Apple/Command key (Mac) while clicking. Interaction types are searched in this hierarchy: ...

Some 30 years after its discovery, phage display remains one of the most widely used methods of in vitro selection. Initially developed to revolutionize the generation of therapeutic antibodies, phage display is now the first choice for screening artificial binding proteins. Artificial binding proteins can be used as reagents to study protein-protein interactions, target posttranslational modifications, and distinguish between homologous proteins. They can also be used as research and affinity reagents, for diagnostic purposes, and as therapeutics. However, the ability to identify isoform-specific reagents remains highly challenging. We describe an adapted phage display protocol using an artificial binding protein (Affimer) for the selection of isoform-selective binding proteins. ...

Proteome is a complement of proteins expressed in a cell at given time and proteomics means global analysis of this protein complement. Proteomics investigates the global changes of proteins in cells and tissues in response to a stimulus (for example temperature change, drug or nutrient treatment, or growth phase). It also studies protein-protein interactions. Proteomics came into prominence after 1997 and quickly became a popular research avenue, holding much greater importance than scientists initially suspected. The main reason for this is the fact that based on the genomic sequence it is impossible to predict how the gene products (proteins) are going to behave. Proteins are regulated at the level of protein translation, subsequently they can be modified by addition of various molecules (sugar, for example). Proteins can have varying half-lives, and their intracellular distribution can be predicted only with limited certainty.. ...

Background Schizophrenia (SZ) is a heritable, complex mental disorder. We have seen limited success in finding causal genes for schizophrenia from numerous conventional studies. Protein interaction network and pathway-based analysis may provide us an alternative and effective approach to investigating the molecular mechanisms of schizophrenia. Methodology/Principal Findings We selected a list of schizophrenia candidate genes (SZGenes) using a multi-dimensional evidence-based approach. The global network properties of proteins encoded by these SZGenes were explored in the context of the human protein interactome while local network properties were investigated by comparing SZ-specific and cancer-specific networks that were extracted from the human interactome. Relative to cancer genes, we observed that SZGenes tend to have an intermediate degree and an intermediate efficiency on a perturbation spreading throughout the human interactome. This suggested that schizophrenia might have different pathological

Video articles in JoVE about g2 phase include Cell Cycle Analysis in the C. elegans Germline with the Thymidine Analog EdU, Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols, Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM), Analysis of Combinatorial miRNA Treatments to Regulate Cell Cycle and Angiogenesis.

This protein protein interaction antibody pair set comes with two antibodies to detect the protein-protein interaction, one against the NEFL protein, and the other against the APP protein for use in in situ Proximity Ligation Assay. See Publication Reference below. (DI0062) - Products - Abnova

This protein protein interaction antibody pair set comes with two antibodies to detect the protein-protein interaction, one against the HGF protein, and the other against the MET protein for use in in situ Proximity Ligation Assay. See Publication Reference below. (DI0046) - Products - Abnova

Wiki-Pi: a web resource for human protein-protein interactions. It shows genes and PPIs with information about pathways, protein-protein interactions (PPIs), Gene Ontology (GO) annotations including cellular localization, molecular function and biological process, drugs, diseases, genome-wide association studies (GWAS), GO enrichments, PDB ID, Uniprot ID, HPRD ID, and word cloud from pubmed abstracts.

Wiki-Pi: a web resource for human protein-protein interactions. It shows genes and PPIs with information about pathways, protein-protein interactions (PPIs), Gene Ontology (GO) annotations including cellular localization, molecular function and biological process, drugs, diseases, genome-wide association studies (GWAS), GO enrichments, PDB ID, Uniprot ID, HPRD ID, and word cloud from pubmed abstracts.

Significance Analysis of INTeractome (SAINT) is a software package for scoring protein‐protein interactions based on label‐free quantitative proteomics data (e

BRIEF DESCRIPTION:. The PhD student post will be part of an interdisciplinary team working on the quantitative and systems analysis of signaling networks in colon cancer. This study is funded through Science Foundation Ireland (SFI). The project will investigate how signalling and protein interaction networks are context-specific quantitatively modulated in (patho)physiologically-relevant primary cells and in vivo-like 3D model systems. Specifically, we will study how protein interactions control cellular phenotypes by investigating (i) how they generate cell type specific vs. general functions; (ii) how pathogenic mutations affect these interactions and downstream signalling; and (iii) how signal flow changes can be validated by generating mutations that rewire networks in a designed fashion.. The student will gain valuable knowledge in the analysis of signal transduction networks in colon cancer, protein analysis techniques, and standard methods used in molecular and cell biology. The student ...

BACKGROUND: Human protein-protein interaction (PPI) data is essential to network and systems biology studies. PPI data can help biochemists hypothesize how proteins form complexes by binding to each other, how extracellular ...

The superiority of KNN over KM is not surprising. With KNN, a protein of interest is clustered with the top K most signature-similar proteins in the network. With KM, a protein of interest is clustered with a signature-closest centre protein, i.e. with the centre protein having the highest signature similarity with it (see §3). However, the signature-closest centre protein is not necessarily the most signature-similar protein in the network. Additionally, KNN allows for overlap between clusters, whereas KM does not. Thus, with KNN, known cancer genes can be positioned in multiple clusters, and therefore the number of possible clusters that are significantly enriched with cancer genes might be higher for KNN than for KM. Additionally, proteins perform the function or participate in a disease by interacting with other proteins within a functional module, but also with proteins across modules. Thus, it might be biologically relevant to allow for the overlap between clusters. The better performance ...

Creative Biolabs offers high-throughput X-ray crystallography or Protein crystallography services for protein-protein interaction assays.

Graphs provide a natural framework for visualizing and analyzing networks of many types, including biological networks. Network clustering is a valuable approach for summarizing the structure in large networks, for predicting unobserved interactions, and for predicting functional annotations. Many current clustering algorithms suffer from a common set of limitations: poor resolution of top-level clusters; over-splitting of bottom-level clusters; requirements to pre-define the number of clusters prior to analysis; and an inability to jointly cluster over multiple interaction types. A new algorithm, Hierarchical Agglomerative Clustering (HAC), is developed for fast clustering of heterogeneous interaction networks. This algorithm uses maximum likelihood to drive the inference of a hierarchical stochastic block model for network structure. Bayesian model selection provides a principled method for collapsing the fine-structure within the smallest groups, and for identifying the top-level groups within a

Thank you for your interest in spreading the word about Biochemical Society Transactions.. NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.. ...

Understanding the underlying architecture of gene regulatory networks (GRNs) has been one of the major goals in systems biology and bioinformatics as it can provide insights in disease dynamics and drug development. Such GRNs are characterized by their scale-free degree distributions and existence of network motifs, which are small subgraphs of specific types and appear more abundantly in GRNs than in other randomized networks. In fact, such motifs are considered to be the building blocks of GRNs (and other complex networks) and they help achieve the underlying robustness demonstrated by most biological networks. The goal of this thesis is to design biological network (specifically, GRN) growing models. As the motif distribution in networks grown using preferential attachment based algorithms do not match that of the GRNs seen in model organisms like E. coli and yeast, we hypothesize that such models at a single node level may not properly reproduce the observed degree and motif distributions of

Keratin, type I cuticular Ha1 is a protein that in humans is encoded by the KRT31 gene. The protein encoded by this gene is a member of the keratin gene family. As a type I hair keratin, it is an acidic protein which heterodimerizes with type II keratins to form hair and nails. The type I hair keratins are clustered in a region of chromosome 17q12-q21 and have the same direction of transcription. Model organisms have been used in the study of KRT31 function. A conditional knockout mouse line called Krt31tm1e(KOMP)Wtsi was generated at the Wellcome Trust Sanger Institute. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Additional screens performed: - In-depth immunological phenotyping ENSG00000262993 GRCh38: Ensembl release 89: ENSG00000094796, ENSG00000262993 - Ensembl, May 2017 GRCm38: Ensembl release 89: ENSMUSG00000048981 - Ensembl, May 2017 Human PubMed Reference:. Mouse PubMed Reference:. Fink P, Rogers MA, Korge B, Winter H, ...

Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, OConnor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D (2007). Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3: 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931 ...

Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, OConnor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D (2007). Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3: 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931 ...

TY - JOUR. T1 - Organized Modularity in the Interactome: Evidence from the Analysis of Dynamic Organization in the Cell Cycle. AU - Wang, Haiying. AU - Zheng, Huiru. PY - 2014/12/4. Y1 - 2014/12/4. N2 - The organization of global protein interaction networks (PINs) has been extensively studied and heatedly debated. We revisited this issue in the context of the analysis of dynamic organization of a PIN in the yeast cell cycle. Statistically significant bimodality was observed when analyzing the distribution of the differences in expression peak between periodically expressed partners. A close look at their behavior revealed that date and party hubs derived from this analysis have some distinct features. There are no significant differences between them in terms of protein essentiality, expression correlation and semantic similarity derived from Gene Ontology (GO) biological process hierarchy. However, date hubs exhibit significantly greater values than party hubs in terms of semantic similarity ...

Modules that switch protein-protein interactions on and off are important to develop artificial biology; for instance, to assemble orthogonal signaling pathways, to manage synthetic protein constructions dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system {couples} nucleotide-dependent switching of MinD dimerization to membrane targeting to set off spatiotemporal sample formation. Here …. De novo design of a reversible phosphorylation-dependent switch for membrane targeting Read More ». ...

A challenge for biomedical scientists today is to arrive at an understanding of cellular behavior on a global scale. The advent of DNA microarrays has greatly facilitated discovery of gene expression profiles associated with different cellular states. The problem of understanding cellular signaling at the level of the interacting proteins is in some ways more challenging. Ashman et al. discuss the current methods available for studying protein interactions on a global scale, as well as directions for the future. Technical hurdles exist at many stages, from the isolation of protein complexes, to the determination of their composition, to the software and databases needed to analyze the results of large-scale, high-throughput datasets. Ashman et al. suggest that, with advances in technology and cooperation among academia and industry, a global protein interaction map that underlies cellular behavior will emerge as an essential resource for basic and applied research.. ...

The discovery of new Protein-Protein Interaction (PPI) modulators is currently limited by the difficulties associated with the design and synthesis of selective small molecule inhibitors. Peptides are a potential solution for disrupting PPIs; however, they typically suffer from poor stability in vivo and limited tissue penetration hampering their wide spread use as new chemical biology tools and potential therapeutics. In this work, a combination of CuAAC chemistry, molecular modelling, X-ray crystallography, and biological validation allowed us to develop highly functionalised peptide PPI inhibitors of the protein CK2. The lead peptide, CAM7117, prevents the formation of the holoenzyme assembly in vitro, slows down proliferation, induces apoptosis in cancer cells and is stable in human serum. CAM7117 could aid the development of novel CK2 inhibitors acting at the interface and help to fully understand the intracellular pathways involving CK2. Importantly, the approach adopted herein could be ...

Homopolymeric amino acids repeats (AARs), which are widespread in proteomes, have often been viewed simply as spacers between protein domains, or even as junk sequences with no obvious function but with a potential to cause harm upon expansion as in genetic diseases associated with polyglutamine or polyalanine expansions, including Huntington disease and cleidocranial dysplasia. A growing body of evidence indicates however that at least some AARs can form organized, functional protein structures and can regulate protein function. In particular, certain AARs can mediate protein-protein interactions, either through homotypic AAR-AAR contacts or through heterotypic contacts with other protein domains. It is still unclear however, whether AARs may have a generalized, proteome-wide role in shaping protein-protein interaction networks. Therefore, we have undertaken here a bioinformatics screening of the human proteome and interactome in search of quantitative evidence of such a role. We first identified the

When a cell is perturbed by external stimuli, it responds by adjusting the amount at which different types of proteins are needed. Transcriptional regulatory networks form the core of this cellular response system. However, the static wiring of these networks does not reveal which parts of the network are active under certain conditions and how perturbations are propagated through the network. For this reason there has been much interest in integrating the static network topology with gene expression data which reflect the dynamical or functional state of the network. In a pioneering paper, large changes were identified in the subnetworks of the transcriptional regulatory network of S. cerevisiae active under five different conditions [1]. In reality, the transcriptional regulatory network cannot be considered in isolation, but it is integrated with other networks such as the protein-protein interaction network [2]. In [3], a framework was developed which integrates protein-protein and ...

We have initiated an effort to exhaustively map interactions between HTLV-1 Tax and host cellular proteins. The resulting Tax interactome will have significant utility toward defining new and understanding known activities of this important viral protein. In addition, the completion of a full Tax interactome will also help shed light upon the functional consequences of these myriad Tax activities. The physical mapping process involved the affinity isolation of Tax complexes followed by sequence identification using tandem mass spectrometry. To date we have mapped 250 cellular components within this interactome. Here we present our approach to prioritizing these interactions via an in silico culling process. We first constructed an in silico Tax interactome comprised of 46 literature-confirmed protein-protein interactions. This number was then reduced to four Tax-interactions suspected to play a role in DNA damage response (Rad51, TOP1, Chk2, 53BP1). The first-neighbor and second-neighbor interactions of

Self-interacting proteins (SIPs) play an essential role in cellular functions and the evolution of protein interaction networks (PINs). Due to the limitations of experimental self-interaction proteins detection technology, it is a very important task to develop a robust and accurate computational approach fo

Associate Professor of Biomedical Informatics and Intelligent Systems, University of Pittsburgh - Cited by 1,733 - Translational Bioinformatics - Networks Analysis - Machine Learning - Protein-Protein Interaction Prediction

Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect

Research Interest. Proteomics describes the study and characterization of complete set of proteins present in a cell, organ or organism at a given time. My laboratory is using high throughput proteomic techniques such as two-dimensional difference in gel electrophoresis, mass spectrometry and protein microarray etc. for biomarker discovery in cancer & tropical diseases of India such as malaria, to study protein-protein interactions and drug target discovery. Information obtained from research program is also used for in silico studies and computing models to enhance our understanding in systems approach.. Academic Background. ...

TY - JOUR. T1 - Advances in cell-free protein array methods. AU - Yu, Xiaobo. AU - Petritis, Brianne. AU - Duan, Hu. AU - Xu, Danke. AU - LaBaer, Joshua. PY - 2018/1/2. Y1 - 2018/1/2. N2 - Introduction: Cell-free protein microarrays represent a special form of protein microarray which display proteins made fresh at the time of the experiment, avoiding storage and denaturation. They have been used increasingly in basic and translational research over the past decade to study protein-protein interactions, the pathogen-host relationship, post-translational modifications, and antibody biomarkers of different human diseases. Their role in the first blood-based diagnostic test for early stage breast cancer highlights their value in managing human health. Cell-free protein microarrays will continue to evolve to become widespread tools for research and clinical management. Areas covered: We review the advantages and disadvantages of different cell-free protein arrays, with an emphasis on the methods ...

Social deficit is one of the core symptoms of neuropsychiatric diseases, in which immune genes play an important role. Although a few immune genes have been shown to regulate social and emotional behaviors, how immune gene network(s) may jointly regulate sociability has not been investigated so far. To decipher the potential immune-mediated mechanisms underlying social behavior, we first studied the brain microarray data of eight inbred mouse strains with known variations in social behavior and retrieved the differentially expressed immune genes. We then made a protein-protein interaction analysis of them to find the major networks and explored the potential association of these genes with the behavior and brain morphology in the mouse phenome database. To validate the expression and function of the candidate immune genes, we selected the C57BL/6 J and DBA/2 J strains among the eight inbred strains, compared their social behaviors in resident-intruder and 3-chambered social tests and the mRNA levels of

In this work, we have analyzed the influence of cation-pi interactions to the stability of Sm/LSm assemblies and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher than phenylalanine and tyrosine in the pi group. Arg-Tyr interactions are predominant among the various pairs analyzed. The furcation level of multiple cation-pi interactions is much higher than that of single cation-pi interactions in Sm/LSm interfaces. We have found hot spot residues forming cation-pi interactions, and hot spot composition is similar for all aromatic residues. The Arg-Phe pair has the strongest interaction energy of -8.81 kcal mol(-1) among all the possible pairs of amino acids. The extent of burial of the residue side-chain correlates with the Delta Delta G of binding for residues in the core and also for hot spot residues cation-pi bonded across the interface. Secondary structure of the cation...-pi ...

Reductionist philosophy has directed biological research for decades [1, 2]. A significant amount of information has been generated so far in the field of biological sciences as enrichment of human knowledgebase to understand life [1]. Despite enormous success of reductionism to decode the structural and functional attributes at cellular and molecular levels of life-organization, it is progressively becoming clearer that biological functions can rarely be credited to discrete perception of individual molecules. Alternatively, most biological phenomena emerge due to extremely interactive complexity derived from functional integrity of cells numerous constituents [2]. Various recent approaches have been initiated and accomplished to study biological systems in more integrative and comprehensive way. Network model can play an important role to understand the complex network system based on multiple sets of interactions and to make plain and clear analysis of the origin of observed network ...

Lilia Iakoucheva is an Editor at PeerJ. Bio: Assistant Professor in the Department of Psychiatry at the University of California San Diego, USA. Currently investigates the molecular basis of neurodevelopmental and psychiatric diseases using genomic and systems biology approaches. Dr. Iakouchevas research focuses on understanding of the molecular basis of autism and schizophrenia using systems biology approaches. The aim is to discover functional protein interaction networks connecting seemingly unrelated candidate genes for psychiatric diseases. Dr. Iakouchevas lab is building comprehensive protein-protein interaction networks for autism and schizophrenia candidate genes and their splicing isoforms. In addition, they are integrating gene expression data with our experimentally derived networks to understand spatio-temporal dynamics of protein interactions in the brain. Their immediate goal is to investigate perturbations of the disease networks by the Copy Number Variants (CNVs) and protein

Interaction Profile: Persistent Chemicals found in Breast Milk. The ATSDR Interaction Profile succintly characterizes the toxicologic and adverse health effects information for mixtures of hazardous substances. Each peer-reviewed profile identifies and reviews the key literature that describes toxicologic properties of the featured mixtures.

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscapes software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene

The active forward movement of cells is often associated with the rearward transport of particles over the surfaces of their lamellae. Unlike the rest of the lamella, we found that the leading edge (within 0.5 microns of the cell boundary) is specialized for rearward transport of membrane-bound particles, such as Con A-coated latex microspheres. Using a single-beam optical gradient trap (optical tweezers) to apply restraining forces to particles, we can capture, move and release particles at will. When first bound on the central lamellar surface, Con A-coated particles would diffuse randomly; when such bound particles were brought to the leading edge of the lamella with the optical tweezers, they were often transported rearward. As in our previous studies, particle transport occurred with a concurrent decrease in apparent diffusion coefficient, consistent with attachment to the cytoskeleton. For particles at the leading edge of the lamella, weak attachment to the cytoskeleton and transport ...

TY - JOUR. T1 - Approaches to Investigating the Protein Interactome of PTEN. AU - Smith, Sarah L.. AU - Pitt, Andrew R.. AU - Spickett, Corinne M.. N1 - This document is the Accepted Manuscript version of a Published Work that appeared in final form in J. Proteome Res, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jproteome.0c00570 Funding: This project has received funding from Aston University (UK) and the European Unions Horizon 2020 research and innovation program under the Marie Sklowdowska-Curie Grant Agreement No. 675132 www.masstrplan.org. PY - 2020/10/19. Y1 - 2020/10/19. N2 - The tumor suppressor phosphatase and tensin homologue (PTEN) is a redox-sensitive dual specificity phosphatase with an essential role in the negative regulation of the PI3K-AKT signaling pathway, affecting metabolic and cell survival processes. PTEN is commonly mutated in cancer, and ...

Products for analysis of protein interactions include pull-down assays, and BRET-based and complementation reporter based systems. GST pull-down systems are used in traditional methods based on cell extracts and/or cell free expression. The HaloTag® Mammalian Pull-Down System is used to isolate and identify intracellular protein complexes from mammalian cells. NanoBRET™ technology uses bioluminescence resonance energy transfer (BRET) in a proximity-based assay that detects protein interactions by measuring energy transfer from a bioluminescent protein donor to a fluorescent protein acceptor. NanoBiT assays rely on a two-subunit system based on NanoLuc® luciferase that can be used for intracellular detection of protein:protein interactions. The subunits are fused to proteins of interest, forming a functional enzyme that generates a bright, luminescent signal when the proteins interact.

FUNCTIONS IN MOLECULAR_FUNCTION UNKNOWN INVOLVED IN BIOLOGICAL_PROCESS UNKNOWN EXPRESSED IN 18 PLANT STRUCTURES EXPRESSED DURING 9 GROWTH STAGES CONTAINS INTERPRO DOMAIN/S PROTEIN OF UNKNOWN FUNCTION DUF618 (INTERPROIPR006903) REGULATION OF NUCLEAR PRE-MRNA PROTEIN (INTERPROIPR006569) ENTH/VHS (INTERPROIPR008942) BEST ARABIDOPSIS THALIANA PROTEIN MATCH IS UNKNOWN PROTEIN (TAIRAT5G100601) HAS 3523 BLAST HITS TO 3241 PROTEINS IN 333 SPECIES ARCHAE - 25 BACTERIA - 251 METAZOA - 1575 FUNGI - 421 PLANTS - 142 VIRUSES - 17 OTHER EUKARYOTES - 1092 (SOURCE NCBI BLINK ...

FUNCTIONS IN MOLECULAR_FUNCTION UNKNOWN INVOLVED IN UBIQUITIN-DEPENDENT PROTEIN CATABOLIC PROCESS LOCATED IN CHLOROPLAST EXPRESSED IN CULTURED CELL CONTAINS INTERPRO DOMAIN/S MOV34/MPN/PAD-1 (INTERPROIPR000555) BEST ARABIDOPSIS THALIANA PROTEIN MATCH IS UNKNOWN PROTEIN (TAIRAT4G161441) HAS 753 BLAST HITS TO 752 PROTEINS IN 167 SPECIES ARCHAE - 0 BACTERIA - 0 METAZOA - 359 FUNGI - 199 PLANTS - 115 VIRUSES - 0 OTHER EUKARYOTES - 80 (SOURCE NCBI BLINK ...

Protein fragment complementation assays for high-throughput and high-content screening - The present invention provides protein fragment complementation assays for drug discovery, in particular to identify compounds that activate or inhibit cellular pathways. Based on the selection of an interacting protein pair combined with an appropriate PCA reporter, the assays may be run in high-throughput or high-content mode and may be used in automated screening of libraries of compounds. The interacting pair may be selected by cDNA library screening; by gene-by-gene interaction mapping; or by prior knowledge of a pathway. Fluorescent and luminescent assays can be constructed using the methods provided herein. The selection of suitable PCA reporters for high-throughput or high-content (high-context) assay formats is described for a diversity of reporters, with particular detail provided for examples of monomeric enzymes and fluorescent proteins. Methods are described for constructing such assays for one ...

Network approaches have demonstrated their potential impact on health-related research, including gene/protein characterization and drug design and side effects (14, 18, 19, 22, 36, 52), yet demonstrations that network information can inform drug target discovery are still limited. Here, we present the first confirmation that virus and host protein interaction data can be integrated to improve large-scale drug target discovery (specifically antiviral target discovery) and reveal additional insights into virus-host interactions. The positions of virus-interacting proteins suggest that the influenza virus has evolved to interact with proteins that influence network behavior, regardless of known abundance-degree biases in PPI data generation (which has not previously been demonstrated). The virus-specific subnetwork reveals that there is a set of proteins with moderately high betweenness in the total network yet low betweenness in the subnetwork. While these proteins may be of high importance to ...

Dengue virus manipulates cellular processes to its advantage through specific interactions with the hosts protein interaction network. The interaction networks presented here provide a set of hypothesis for further experimental investigation into the DENV life cycle as well as potential therapeutic …

starBase v2.0 for decoding miRNA-mRNA, miRNA-ceRNA, miRNA-lncRNA, miRNA-circRNA, miRNA-pseudogene and protein-RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data.. starBase v2.0 also provides visualization, analysis, discovery and downloading of above-mentioned large-scale functional genomics data.. miRNA-lncRNA interaction Descriptions. You can browse the predicted miRNA-lncRNA interactions by scanning lncRNA sequences overlapping with CLIP-Seq peaks for potential microRNA targets (6mer-8mer) and then output the detail informations. Here, we just list the predicted miRNA-target interactions overlapped with CLIP-Seq data.. lncRNABase. Li JH, Liu S, Zhou H, Qu LH* and Yang JH*. (2013) starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Submitted.. ...

The rapid onset of resistance to new drugs and emergence of antibiotic resistant bacteria has led to resurgence in life-threatening bacterial infections. These problems have revitalized interest in antibiotics and lead to new research. To gain further ins

1.1. BioGrid Australia provides the prospective member with the following documents: • BioGrid Australia Limited Constitution; • The Collaboration Agreement Establishing the BioGrid Australia Collaboration (and all Schedules and Annexure) (Collaboration Agreement[1]); • An Application Form to join as a member of BioGrid Australia Limited; and, • Deed of Accession to join the BioGrid Australia Collaboration Agreement.. 1.2. The prospective member completes and executes (i.e. signs) and returns to BioGrid Australia: • Application Form to join BioGrid Australia Limited as a Member; and • Deed of Accession to join the BioGrid Australia Collaboration Agreement.. 1.3. The Management Committee (of the BioGrid Australia Collaboration Agreement) then considers the Deed of Accession signed by the prospective member. The Management Committee is required to pass a unanimous resolution consenting to the admission of the prospective member ...

In recent years, various types of cellular networks have penetrated biology and are nowadays used omnipresently for studying eukaryote and prokaryote organisms. Still, the relation and the biological overlap among phenomenological and inferential gene networks, e.g., between the protein interaction network and the gene regulatory network inferred from large-scale transcriptomic data, is largely unexplored. We provide in this study an in-depth analysis of the structural, functional and chromosomal relationship between a protein-protein network, a transcriptional regulatory network and an inferred gene regulatory network, for S. cerevisiae and E. coli. Further, we study global and local aspects of these networks and their biological information overlap by comparing, e.g., the functional co-occurrence of Gene Ontology terms by exploiting the available interaction structure among the genes. Although the individual networks represent different levels of cellular interactions with global structural and

The figure at the left displays the protein interaction network for human AQP2(red dot in center) as generated using STRING (4). Below is a pie chart depicting the biological processes that the proteins identified in this network are involved in. The ontologies of these interactors were visualized using PANTHER (5). The most dominant functional categories of the interacting proteins are involvement in cellular processes(including signal transduction), localization(including transport), multicellular organism processes, and biological regulation. One result of note is the inclusion of several other aquaporins within this network, including AQP1, AQP3, and AQP4. This opens the possibility for some overlap in coregulation of these different aquaporins ...

Most of the work in this area has focused on mapping protein-protein interactions (e.g., see Stanyon and Finley, 2000; Zhong et al., 2003; Giot, 2003; Stanyon et al., 2004; Parrish et al., 2007). A long running project has been to construct and characterize a proteome-wide interaction map for Drosophila. This project entails conducting high throughput screens, developing computational tools to analyze interaction data, and sharing the interaction data and analysis tools with the public via a web-accessible database (www.DroIDb.org). We have also been concerned with figuring out how to use the flood of functional genomic data from our own and other studies to create systems-wide models of biological processes. In addition to the public database and network analysis interfaces (Murali et al., 2011; Pacifico et al., 2006; Yu et al., 2008), the lab has developed computational methods to analyze interaction networks (Murali et al., 2014), to predict new protein interactions (Yu et al., 2005), to ...

DroID is a comprehensive gene and protein interactions (interactome) database designed specifically for the model organism Drosophila. The database includes protein-protein, TF-gene, miRNA-gene, and genetic interactions.. Begin by searching for genes of interest below. You will then be able to search for interactions involving your genes. For more advanced searches and dynamic graphing capabilities, try IM Browser or the DroID Cytoscape plugin.. ...

To test the efficacy of this model, we needed networks with large numbers of known protein-protein interactions. A complication in this process arises in that, even if a large number of interactions are known, not all of them have a defined domain composition. For this work, we used Saccharomyces cerevisiae protein-protein interactions taken from the DIP (http://dip.doe-mbi.ucla.edu/; Xenarioset al. 2000). We determined the domains involved in each interaction by analyzing protein sequences with hmmpfam (Batemanet al. 2000), a publicly available software tool that referenced 2015 domains at the time of this analysis. We analyzed a total of 642 protein-protein interactions (all with at least 1 domain) and then used them to determine the domain-domain interaction probabilities. Data (in this case a list of undirected protein-protein interactions) used for studying the effect of vertex removal on network edge distributions were taken from the Fields Lab home page ...

A polypeptide chain of a protein-protein complex is said to be obligatory if it is bound to another chain throughout its functional lifetime. Such a chain might not adopt the native fold in the unbound form. A non-obligatory polypeptide chain associates with another chain and dissociates upon molecular stimulus. Although conformational changes at the interaction interface are expected, the overall 3-D structure of the non-obligatory chain is unaltered. The present study focuses on protein-protein complexes to understand further the differences between obligatory and non-obligatory interfaces. A non-obligatory chain in a complex of known 3-D structure is recognized by its stable existence with same fold in the bound and unbound forms. On the contrary, an obligatory chain is detected by its existence only in the bound form with no evidence for the native-like fold of the chain in the unbound form. Various interfacial properties of a large number of complexes of known 3-D structures thus classified are

Purified U2OS PRβ Protein Interaction Assay Kit from Creative Biomart. U2OS PRβ Protein Interaction Assay Kit can be used for research.

Purified U2OS PRα Protein Interaction Assay Kit from Creative Biomart. U2OS PRα Protein Interaction Assay Kit can be used for research.

Lehner B، Semple JI، Brown SE، وآخرون. (2004). Analysis of a high-throughput yeast two-hybrid system and its use to predict the function of intracellular proteins encoded within the human MHC class III region. Genomics. 83 (1): 153-67. PMID 14667819. doi:10.1016/S0888-7543(03)00235-0. ...

Recent genome analyses revealed intriguing correlations between variables characterizing the functioning of a gene, such as expression level (EL), connectivity of genetic and protein-protein interaction networks, and knockout effect, and variables describing gene evolution, such as sequence evolution rate (ER) and propensity for gene loss. Typically, variables within each of these classes are positively correlated, e.g. products of highly expressed genes also have a propensity to be involved in many protein-protein interactions, whereas variables between classes are negatively correlated, e.g. highly expressed genes, on average, evolve slower than weakly expressed genes. Here, we describe principal component (PC) analysis of seven genome-related variables and propose biological interpretations for the first three PCs. The first PC reflects a genes importance, or the status of a gene in the genomic community, with positive contributions from knockout lethality, EL, number of protein-protein ...

Although outer hair cells (OHCs) play a key role in cochlear amplification, it is not fully understood how they amplify sound signals by more than 100 fold. Two competing or possibly complementary mechanisms, stereocilia-based and somatic electromotility-based amplification, have been considered. Lacking knowledge about the exceptionally rich protein networks in the OHC plasma membrane, as well as related protein-protein interactions, limits our understanding of cochlear function. Therefore, we focused on finding protein partners for two important membrane proteins: Cadherin 23 (cdh23) and prestin. Cdh23 is one of the tip-link proteins involved in transducer function, a key component of mechanoelectrical transduction and stereocilia-based amplification. Prestin is a basolateral membrane protein responsible for OHC somatic electromotility. Using the membrane-based yeast two-hybrid system to screen a newly built cDNA library made predominantly from OHCs, we identified two completely different groups of

Viral capsids are composed of multiple copies of one or a few gene products that self-assemble on their own or in the presence of the viral genome and/or auxiliary proteins into closed shells (capsids). We have analyzed 75 high-resolution virus capsid structures by calculating the average fraction of the solvent-accessible surface area of the coat protein subunits buried in the viral capsids. This fraction ranges from 0 to 1 and represents a normalized protein-protein interaction (PPI) index and is a measure of the extent of protein-protein interactions. The PPI indices were used to compare the extent of association of subunits among different capsids. We further examined the variation of the PPI indices as a function of the molecular weight of the coat protein subunit and the capsid diameter. Our results suggest that the PPI indices in T=1 and pseudo-T=3 capsids vary linearly with the molecular weight of the subunit and capsid size. This is in contrast to quasi-equivalent capsids with T>or=3, ...

Random graphs are at the forefront of applied probability,, and a central topic in multidisciplinary science where mathematical ideas are used to model and understand the real world. The aim of this course is four-fold: present novel models to describe real-world networks, and their topological properties; study their local behavior; discuss networks functionality, as described by stochastic processes on them; and discuss several statistical problems of networks and their functionality, including community detection, estimation of preferential attachment functions, estimation of the source of an epidemic. The school will present basic material in the first week, while the second week will contain more advanced material, at the forefront of science.. The Bocconi Summer School in Statistics and Probability is offered by Bocconi University, Milano, and is hosted by the Lake Como School of Advanced Studies. The aim of the School is to establish a track of high level courses on cutting-edge topics in ...

The BiBiServ team discontinued the online service for AGt_SDP. Please contact the author(s) of AGT-SDP for any questions concerning AGT-SDP. In unbound protein--protein docking, the complex of two proteins is predicted using the unbound conformations of the proteins (Halperin et al.,2002). For testing of docking algorithms, two unbound proteins which form a known complex have to be identified, so that the result of the docking algorithm can be compared to the known complex. For the identification of test cases, the structures taken from the PDB have to be classified as unbound proteins or complexes and unbound proteins with a 100% sequence identity to one complex part have to be searched. By now, most groups use handpicked test sets. The largest collection of test cases used so far is described by Chen et al. (Chen et al.,2003) and contains 31 test cases for unbound docking. Because of the exponential growth of available protein structures in the PDB, automatic generation of test cases will ...

The BiBiServ team discontinued the online service for AGt_SDP. Please contact the author(s) of AGT-SDP for any questions concerning AGT-SDP. In unbound protein--protein docking, the complex of two proteins is predicted using the unbound conformations of the proteins (Halperin et al.,2002). For testing of docking algorithms, two unbound proteins which form a known complex have to be identified, so that the result of the docking algorithm can be compared to the known complex. For the identification of test cases, the structures taken from the PDB have to be classified as unbound proteins or complexes and unbound proteins with a 100% sequence identity to one complex part have to be searched. By now, most groups use handpicked test sets. The largest collection of test cases used so far is described by Chen et al. (Chen et al.,2003) and contains 31 test cases for unbound docking. Because of the exponential growth of available protein structures in the PDB, automatic generation of test cases will ...

The combined use of gene expression profiles and protein-protein interaction networks has shown remarkable successes in the prediction of breast cancer met

Radioresistance is one of the main obstacle limiting the therapeutic efficacy and prognosis of patients, the molecular mechanisms of radioresistance is still unclear. The purpose of this study was to identify the key genes and miRNAs and to explore their potential molecular mechanisms in radioresistant nasopharyngeal carcinoma. In this study, we analysis the differentially expressed genes and microRNA based on the database of GSE48501 and GSE48502, and then employed bioinformatics to analyze the pathways and GO terms in which DEGs and DEMS target genes are involved. Moreover, Construction of protein-protein interaction network and identification of hub genes. Finally, analyzed the biological networks for validated target gene of hub miRNAs. A total of 373 differentially expressed genes (DEGs) and 14 differentially expressed microRNAs (DEMs) were screened out. The up-regulated gene JUN was overlap both in DEGs and publicly available studies, which was potentially targeted by three miRNAs, including hsa

New type of protein-protein interaction: actomyosin gels interact in a THRESHOLD manner. For details see the following paper: V.V.Matveev. Evidence of a new type of protein-protein interaction: desensitized actomyosin blocks Ca2+-sensitivity of the natural one. A possible model for an intracellular signalling system related to actin filaments. Physiological Chemistry Physics & Medical NMR, 32: 167-179, 2000. ABSTRACT see here: http://members.nbci.com/vm_spb/actomyosin/signal.htm Sent via Deja.com http://www.deja.com/ Before you buy ...

The YRC PDR provides for the searching of millions of protein descriptions from many databases to find proteins and public experimental data describing those proteins produced by the YRC. The experimental data is in the form of mass spectrometry, yeast two-hybrid, protein structure prediction, light microscopy and protein complex predictions.

The YRC PDR provides for the searching of millions of protein descriptions from many databases to find proteins and public experimental data describing those proteins produced by the YRC. The experimental data is in the form of mass spectrometry, yeast two-hybrid, protein structure prediction, light microscopy and protein complex predictions.

The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.

Objective To investigate the function and differentiation of 1/17 type helper T (Th1/17) cells. Methods Bioinformatics analysis was performed using a gene chip dataset (GSE104021) in GEO which contains gene expression data from Th17 cells and Th1/17 cells of healthy human subjects. Taking Th17 cells as the control, R language software was used to analyze the differentially expressed genes (DEGs) between Th17 cells and Th1/17 cells, so as to explore the main functional molecules of Th1/17 cells. After that, gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) analysis of DEGs were conducted by R language software. Finally, the genes enriched into the target biological process in the GO analysis were selected for protein-protein interaction network (PPI) analysis to explore the differentiation process of Th1/17 cells. Results Analysis of DEGs showed that, compared with Th17 cells, the underexpressed genes in Th1/17 cells were interleukin 17A (IL-17A) and C-C motif ...

Objective To investigate the function and differentiation of 1/17 type helper T (Th1/17) cells. Methods Bioinformatics analysis was performed using a gene chip dataset (GSE104021) in GEO which contains gene expression data from Th17 cells and Th1/17 cells of healthy human subjects. Taking Th17 cells as the control, R language software was used to analyze the differentially expressed genes (DEGs) between Th17 cells and Th1/17 cells, so as to explore the main functional molecules of Th1/17 cells. After that, gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) analysis of DEGs were conducted by R language software. Finally, the genes enriched into the target biological process in the GO analysis were selected for protein-protein interaction network (PPI) analysis to explore the differentiation process of Th1/17 cells. Results Analysis of DEGs showed that, compared with Th17 cells, the underexpressed genes in Th1/17 cells were interleukin 17A (IL-17A) and C-C motif ...

Proteins and their interaction networks are at the heart of life. Understanding how diverse proteins come together spatially and temporally and how their specific complexes translate into cellular functions is important to understand health and disease but represents a major challenge. Microtubules are filamentous structures fundamentally involved in diverse cellular processes ranging from cell division, motility and polarity to signaling and intracellular transport. They are also key to form centrioles of centrosomes and axonemes of cilia and flagella. Because of their important role for cell survival, the malfunctioning of the microtubule cytoskeleton is associated with several severe human pathologies including cancer and various forms of ciliopathies as well as cardiovascular, infectious and brain diseases. We use X-ray crystallography in combination with biochemical and biophysical methods to investigate how proteins and drugs regulate the structure, function and dynamics of the microtubule ...

Clive DSantos and Aurélia E. Lewis (2012). Functional Proteomics: Mapping Lipid-Protein Interactomes, Integrative Proteomics, Hon-Chiu Eastwood Leung (Ed.), ISBN: 978-953-51-0070-6, InTech, Available from: http://www.intechopen.com/articles/show/title/functional-proteomics-mapping-lipid-protein-interactomes ...