ProteinsTranscriptomeProximal ProteomeAnalysesBioinformaticsAlterationsGenomeAnnotationMethodsExplorationCharacterizationInsightsQuantificationMolecularDynamicsProteomicGenesGenomicsAnalysis revealedAssayResearchMutationsTranscriptomicsPhysiologicalDiversityProteomics dataCrucialStructuralLungCellularExtracellularVariantsStudiesDataStressAdaptationApproachStudyImplicationsProductsIdentificationGene expression
Proteins20
- SVEVs isolated from lyophilized venoms collected from four different species of snakes ( Agkistrodon contortrix contortrix , Crotalus atrox , Crotalus viridis and Crotalus cerberus oreganus ) were analyzed by mass spectrometry-based proteomic, which allowed the identification of proteins belonging to eight main functional protein classes such as SVMPs, serine proteinases, PLA 2 , LAAO, 5′nucleotidase, C-type lectin, CRISP and Disintegrin. (nature.com)
- To identify proteins interacting with alpha A-crystallin (CRYAA) and to investigate the potential role that these protein interactions play in the function of CRYAA using a human proteome (HuProt) microarray. (molvis.org)
- A breakthrough for the identification of the proteome of the presynaptic active zone was the successful employment of antibodies directed against a cytosolic epitope of membrane integral synaptic vesicle proteins for the immunopurification of synaptic vesicles docked to the presynaptic plasma membrane. (mdpi.com)
- Numerous proteins regulating the rearrangement of the cytoskeleton are indicative of the functional and structural dynamics of the presynapse. (mdpi.com)
- 2D-PAGE for proteome studies gives a map of proteins which reflect changes in protein expression levels, as well different isoforms and posttranslational modifications. (hindawi.com)
- Due to the large number of proteins, no protein array platform has yet been designed that covers the entire human placental proteome. (hindawi.com)
- Functional analysis of the dysregulated proteins indicated a significant enrichment of proteins associated with mitochondrial dynamics, cholesterol biogenesis, and protein clearance. (nih.gov)
- In this study, using an isobaric tags for relative and absolute quantitation (iTRAQ ) approach coupled with LC-MS / MS and bioinformatics, the proteomes were analyzed for the crucial three stages covering the fruiting body development of Ophiocordyceps sinensis , including sclerotium (ST), primordium (PR) and mature fruiting body (MF), with a focus on fruiting body development-related proteins and the potential mechanisms of the development. (peerj.com)
- Quantitative proteomics identified candidate host targets for the NSP5 protease, with specific functional cleavage sequences in host proteins CWC22 and FANCD2. (biorxiv.org)
- Since proteins are key regulators of cellular responses, investigations into proteome alterations during stress induction as well as recovery, can provide important information on how plants cope with stress factors. (frontiersin.org)
- However, individual exposure to drought or heat stress did not show the above proteome alterations, indicating that these proteins are specifically required to resist the combinatorial effects of the above two stresses ( Zhao et al. ). (frontiersin.org)
- The proteome, the entire complement of proteins in an organism, evolves over time, adapting to environmental changes and evolutionary pressures. (alliedacademies.org)
- Functional annotations provide insight into the roles and interactions of proteins within a biological context. (alliedacademies.org)
- There is, therefore, a clear interest in studying the complex interactions between hair proteins such as keratins and KAPs from quantitative, qualitative, and functional perspective. (cosmeticsdesign.com)
- There are several methods developed to predict caspase cleavage sites from individual proteins, but currently none of them can be used to predict caspase cleavage sites from multiple proteins or entire proteomes, or to use several classifiers in combination. (biomedcentral.com)
- Heat shock proteins (HSPs) and antioxidant enzymes are the two major classes of functional proteins that are induced during HSR. (frontiersin.org)
- Because the proteome is a continuously changing set of proteins that differs from cell to cell, it is challenging for scientists to capture and study it. (cdc.gov)
- In 2014, scientists developed a draft map of the human proteome , which catalogued proteins encoded by over 17,000 human genes, or about 84% of all protein-coding genes in the human genome. (cdc.gov)
- Several of the proteins are directly related to the functional and morphological characteristics of B-cells, such as cytoskeleton rearrangement and intracellular signalling triggered by the crosslinking of B-cell receptors. (lu.se)
- Peptide analysis identified products from known matrix protease substrates and secretory proteins, which offered functional relevance to immunoinflammatory responses, extracellular matrix remodeling, and receptor interactions. (cdc.gov)
Transcriptome4
- Combining the proteome and transcriptome level analyses led to a new understanding of ALL. (scilifelab.se)
- In conclusion, the proteome and transcriptome correlation results from this study indicate that ion transport plays a critical role in the adaptation of S. paramamosain to sudden reduction in salinity. (hindawi.com)
- In this study, we present integrated quantitative proteome, transcriptome, and methylome analyses of hematopoietic stem cells (HSCs) and four multipotent progenitor (MPP) populations. (lu.se)
- The purpose of this project is to understand how specific types of genetic variants, which traditionally have not been extensively studied, can affect breast cancer risk and tumour characteristics through effects on the transcriptome and proteome. (lu.se)
Proximal Proteome1
- The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2. (mendeley.com)
Analyses2
- Functional enrichment analyses are often used to generate hypotheses regarding the underlying mechanisms revealed in MS-based proteomics datasets (refs). (scripps.edu)
- these analyses are applicable to the functional evaluation of other genes associated with mitochondrial disease. (mendeley.com)
Bioinformatics1
- Over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants in the protein coding regions. (ncbs.res.in)
Alterations3
- Statistical data analysis revealed 65 specific alterations in the proteome of the central synapses at the early onset stage of disease. (nih.gov)
- These changes include developmental and physiological alterations which influence the genome, proteome, and metabolome of the plant. (frontiersin.org)
- A significant portion of the research articles included in this Research Topic investigated proteome level alterations in diverse organ parts of the plant body upon exposure to abiotic stress factors such as drought, salinity, and submergence. (frontiersin.org)
Genome2
- Ascribing functional roles and/or clinical significances to single nucleotide variants identified from a next-generation sequencing study is an important step in genome interpretation. (ncbs.res.in)
- This study provides a comprehensive genome-wide resource for the functional exploration of molecular, cellular, and epigenetic regulation at the top of the hematopoietic hierarchy. (lu.se)
Annotation3
- Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. (ncbs.res.in)
- Functional annotation clustering showed that they belong to cell cycle, organelle or nuclear lumen, protein transport, and DNA binding and repair clusters. (molvis.org)
- Sequenced genomes often reveal interrupted coding sequences that complicate the annotation process and the subsequent functional characterization of the genes. (nih.gov)
Methods2
- Thus, when screening the placental proteome 2D-PAGE is still among the most accepted methods giving the highest coverage although this may soon change. (hindawi.com)
- Our main aims are to 1) provide a detailed understanding of how variants in regulatory motifs control alternative splicing and intron retention, and 2) develop accurate methods for identification of functional synonymous variants. (lu.se)
Exploration2
- In this study, an ETH Zurich team led by Biognosys' scientific advisor and inventor of the LiP-MS technology, Paola Picotti, has spearheaded the exploration of protein functional states in a proteome-wide manner. (biognosys.com)
- Integrating the principles of systems biology with the exploration of proteome evolution offers a comprehensive approach to unraveling the mechanisms underlying adaptation, variation, and the emergence of novel functions in living organisms [ 1 ]. (alliedacademies.org)
Characterization1
- Combining proteomics and transcriptomics allowed in depth platelet proteome characterization, revealing a significant effect of either stimulus on proteome composition. (nature.com)
Insights2
- By reconstructing the evolutionary history of gene duplication events and their impact on the proteome, researchers gain insights into how organisms acquire novel traits and functions [ 4 ]. (alliedacademies.org)
- Detailed functional and molecular profiling of specific stromal and immune cell populations will provide novel insights on the immunobiology of GBM, and may reveal underlying immunosuppressive mechanisms paving the way towards innovative therapeutic approaches. (lu.se)
Quantification1
- We have recently developed a functional enrichment analysis algorithm explicitly for MS-based proteomics data (PSEA-Quant, Lavallée-Adam, M., Rauniyar, N., McClatchy, D.B., Yates J.R. III: PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data. (scripps.edu)
Molecular2
- By mapping these mutations to the proteome and identifying corresponding functional changes, researchers can uncover the molecular mechanisms that have led to the diversification of protein functions [ 3 ]. (alliedacademies.org)
- This approach helps uncover the molecular basis of specific adaptations, shedding light on the selective pressures that have shaped proteome evolution [ 5 ]. (alliedacademies.org)
Dynamics3
- The proteome of the presynaptic active zone controls neurotransmitter release and the short- and long-term structural and functional dynamics of the nerve terminal. (mdpi.com)
- Here, we have investigated the proteome dynamics of central synapses in P14 Smn 2B/- mice, a model of SMA. (nih.gov)
- Quantitative proteomics strategies such as SILAC and iTRAQ have been widely applied to study the dynamics of proteome. (genengnews.com)
Proteomic5
- This technology will enable a direct connection of the gene regulatory networks that drive critical functional proteomic reactions in many cell types, including immune cells, tumor cells, and stem cells. (the-scientist.com)
- Results of this study allowed us to present very extensive proteomic analysis of SUMO-2 sub-proteome and its changes upon heat shock for the first time ever for such a large scale and quality. (europa.eu)
- Systems biology integrates genomic and proteomic data to track the transfer of genetic material across species, revealing how these events have shaped proteomes and contributed to the acquisition of adaptive traits. (alliedacademies.org)
- 2011 ) Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover. (neurotree.org)
- We investigated the proteome profiles of stimulated and nonstimulated Ramos B-cells at eight time points during 5 d and compared the obtained proteomic data to the corresponding data from DNA-microarray studies. (lu.se)
Genes1
- We addressed this issue by experimentally demonstrating the existence of functional disrupted genes in archaeal genomes. (nih.gov)
Genomics2
- Proteome Research: New Frontiers in Functional Genomics. (wikipedia.org)
- The dynamic nature of proteome evolution is a fascinating subject that systems biology aims to dissect by combining various data types, such as genomics, proteomics, and functional annotations [ 2 ]. (alliedacademies.org)
Analysis revealed2
- In silico analysis revealed the presence of resident immature RNAs in resting platelets, characterized by retained introns, while unbiased proteogenomics correlated intron removal by RNA splicing with changes on proteome composition upon activation. (nature.com)
- Principal component and hierarchical clustering analysis revealed that the post-ETI proteome shifted to an intermediate state that was distinct from pre-ETI and healthy controls, even for those achieving normal lung function. (bvsalud.org)
Assay1
- Further, highly functional arrays were obtained providing an assay sensitivity in the pM to fM range. (lu.se)
Research2
Mutations3
- thus, the prediction of functional and/or regulatory impacts of the various mutations using in silico approaches is an important step toward the identification of functionally significant or clinically actionable variants. (ncbs.res.in)
- The proteome is in a state of constant flux due to various factors, including genetic mutations, gene duplications, and lateral gene transfers. (alliedacademies.org)
- Genetic mutations play a pivotal role in driving proteome evolution. (alliedacademies.org)
Transcriptomics1
- Rui Zheng and Patrick Paczkowski will discuss a new, highly multiplexed, simultaneous single cell transcriptomics and functional proteomics platform. (the-scientist.com)
Physiological1
- For any post-translational modification, the same degree of relative change may reflect very different changes in its absolute abundance, and can therefore differ in terms of physiological and functional relevance. (genengnews.com)
Diversity1
- Proteome evolution is a dynamic process that shapes the diversity of life on Earth. (alliedacademies.org)
Proteomics data1
- In this webinar brought to you by IsoPlexis, Rui Zheng, PhD and Patrick Paczkowski, PhD will introduce IsoPlexis' latest technology, Duomic™, which links both transcriptomic and functional proteomics data directly from the same single cell, across many cells in parallel. (the-scientist.com)
Crucial1
- The removal of glycogen from the samples by centrifugation was crucial for the final proteome maps. (hindawi.com)
Structural1
- Integrating peptide-level LiP-MS data with orthogonal information such as phosphorylation enabled the linking of protein structural changes to functional implications. (biognosys.com)
Lung1
- Recent studies have demonstrated functional consequences outside the lung, and in particular on the vasculature. (cdc.gov)
Cellular1
Extracellular1
- The extracellular signaling protein Sonic hedgehog (Shh) requires dual lipidation for functional signaling, whereby N-terminal palmitoylation is performed by the enzyme Hedgehog acyltransferase (Hhat). (imperial.ac.uk)
Variants3
- We discuss the currently available approaches and major challenges from the perspective of protein sequence, structure, function and interactions that require consideration when interpreting the impact of putatively functional variants. (ncbs.res.in)
- Results The functional validation of VUS identified novel variants causing loss of ECHS1 function. (mendeley.com)
- Synonymous variants can still be functional, e.g. through effects on mRNA splicing and stability, as well as the speed of translation and protein folding. (lu.se)
Studies3
- Studies of the human proteome have enabled scientists to track protein synthesis, modification, and degradation over time and across different cell types. (cdc.gov)
- Functional studies show that SFRP3 can inhibit Wnt5a signaling and induce a decrease in migration and invasion. (lu.se)
- According to Shomron 7 (2010), this field of the clinical pharmacology studies the contribution of genomes, transcriptomes and proteomes in determining drug-response phenotypes (safety and efficacy). (bvsalud.org)
Stress1
Adaptation2
- Our findings offer the perspective of proteome to understand the biology of fruiting body development and highland adaptation in O. sinensis , which would inform the big industry of this valuable fungus. (peerj.com)
- Integrating the principles of systems biology into the study of proteome evolution provides a holistic approach to unraveling the intricate mechanisms driving adaptation and variation. (alliedacademies.org)
Approach1
- Evidence-based dietary management of functional gastrointestinal symptoms: the FODMAP approach. (medscape.com)
Study1
- The study of proteome evolution is a journey through the intricate tapestry of life's history. (alliedacademies.org)
Implications1
- Systems biology investigates these events by analyzing gene family expansions and examining the resulting functional implications. (alliedacademies.org)
Products1
- Included in this product is TRANSFAC®, TRANSPATH® and PROTEOME™ products. (mit.edu)
Identification1
Gene expression1
- The effect on gene expression in cases was verified by RNA-seq and proteome analysis. (mendeley.com)