Proteins or molecular genes interfaces databases protein. Medical search. Frequent questions

you will see in a live demonstration how to use the Entrez interface including filters, the advanced search page, and search strategies to collect and download a specific set of records, to narrow the search, and to use the precomputed relationships available in the Entrez system find related sequences, genomic regions, genomic maps, homologous genes and proteins, pathways and expression information. (piug.org)
Briefly, the user provides a KEGG formatted species id for either human, mouse or rat, and the package will download and store species specific ENTREZ gene IDs and map them to their respective KEGG pathways by accessing the KEGG REST API. (univ-lyon1.fr)
Next, the user will identify significantly enriched pathways in two different gene sets, and finally, the user will identify pathways that are differentially enriched between the two gene sets. (univ-lyon1.fr)
A wide variety of databases have also been used to define these pathways (e.g. (univ-lyon1.fr)
The BioSystems database collects information on interacting sets of biomolecules involved in metabolic and signaling pathways, disease states, and other biological processes. (nih.gov)
BioSystems currently contains biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the EcoCyc ( Escherichia coli K-12 MG1655) subset of the BioCyc databases and is designed to accommodate other data in the future. (nih.gov)
When available each record links to detailed diagrams and annotations for individual pathways on the Web sites of the source databases. (nih.gov)
Therefore, the study of IBD must be faced exploiting an integrated and multilevel approach, ranging from genes, transcripts and proteins to pathways altered in affected tissues, and carefully considering their regulatory mechanisms, which may intervene in the pathology onset. (biomedcentral.com)
These lists are commonly analyzed using software tools and databases that map genes to known pathways or construct subnetworks that connect input lists of genes using known protein-protein or other types of molecular interactions [ 1 - 10 ]. (biomedcentral.com)
To cope with these environmental stresses, plants activate defense responses, including the activation of sets of metabolic pathways and genes. (biomedcentral.com)
Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. (baderlab.org)
Hit lists identified by these methods can often span many protein classes and signaling pathways. (biomedcentral.com)
We established a general human molecular knowledge network of over 3.6 million connections (e.g. gene-disease associations, protein-protein interactions) with disease-specific signal transduction (54 pathways) and metabolite (122) information manually curated from the literature. (biomedcentral.com)
Molecular pathways of motor neuron injury in amyotrophic lateral sclerosis. (medlineplus.gov)

Often high throughput omics studies include a functional enrichment analysis to glean biological insight from a list of candidate genes, proteins, metabolites, etc. (univ-lyon1.fr)
One key component of a statistically rigorous functional enrichment analysis is the definition of a background data set that can be used to estimate the number of candidate genes that are 'expected' to be associated with the pathway by chance, e.g., if 5% of genes in the background data set are associated with a pathway then 5% of candidate gene are expected to be associated with the pathway by chance. (univ-lyon1.fr)
This tool provides a list of candidate genes of a query genome potentially involved in a fusion or a fission event. (cns.fr)
As such, the search for candidate genes related to the comorbid conditions of ADHD and DD can help in elucidating the molecular mechanisms underlying the comorbid condition, and can also be useful for genotyping and identifying new drug targets. (biomedcentral.com)
The results can be utilized to plan experiments for the identification of novel candidate genes and search for novel pharmacological targets. (biomedcentral.com)
Gene-based KASP markers were developed for putative candidate genes TaIPK1-2D and TaNAS10-6D. (bvsalud.org)
Based on gene annotations, sequence variations and expression profiles, the phytic acid biosynthesis gene TaIPK1-2D and nicotianamine synthase gene TaNAS10-6D were predicted as candidate genes. (bvsalud.org)
This study investigated the genetic basis of GZnC and GFeC and provided valuable candidate genes and markers for breeding Zn- and Fe-enriched wheat. (bvsalud.org)
In contrast to experiments focusing on a specific gene or gene family, these genome-scale experiments typically result in the identification of a list of candidate genes that are relatively unfamiliar to any single researcher. (biomedcentral.com)
Researchers are then faced with the daunting task of prioritizing these candidate genes for detailed functional and mechanistic studies. (biomedcentral.com)
Consequently, many researchers (and in particular researchers who are investigating candidate genes from genome-wide analyses) end up visiting many different sites for each gene of interest in order to get as complete a picture as possible of gene function. (biomedcentral.com)
Recent advances have been made in the of host factors, polymorphisms, and candidate genes associated characterization of the immune response to low-molecular- with occupational asthma may improve our understanding of weight agents. (cdc.gov)

The goal of diffEnrich is to compare functional enrichment between two experimentally-derived groups of genes or proteins. (univ-lyon1.fr)
Functional enrichment examines whether the number of genes in the list associated with a biological function or particular pathway is more than would be expected by chance. (univ-lyon1.fr)
Furthermore, most functional enrichment analyses involve a single gene list. (univ-lyon1.fr)
This new version of the database (R20, July 2019) includes a major update of data on germline variations and on the functional assessment of mutant proteins. (who.int)
and - basic research, to study the structural and functional aspects of the p53 protein. (who.int)
The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. (nih.gov)
In addition, structural as well as functional aspects of the different classes of membrane proteins are discussed along with an outline of experimental approaches used to achieve an understanding of membrane protein structure and function at a molecular level. (yale.edu)
Genomics describes the determination of the nucleotide sequence and many further analyses to discover functional and structural information on all the genes of an organism. (yale.edu)
Topics include the methods and results of functional and structural gene analysis on a genome-wide scale as well as a discussion of the implications of this research. (yale.edu)
Sequence similarity and database searching / David S. Wishart -- GCG database searching / David J. Heard -- C. Identifying functional and structural sequence elements. (ewubd.edu)
By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs), researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. (biomedcentral.com)
Studies that utilize genome-wide profiling methods which attempt to explain the differences between two or more experimental conditions such as cells treated with a drug vs. control, diseased tissue vs. normal, gene or protein expression at different time points during cellular differentiation or reprogramming, or candidate gene lists harboring mutations associated with a particular disease, produce lists of genes/proteins without apparent functional relationship. (biomedcentral.com)
functional" genes encoding proteins such as late embryogenesis-associated proteins, detoxification enzymes, heat shock proteins and molecular chaperones, which directly protect plants from abiotic stress, and "regulatory" genes encoding proteins such as protein kinases and transcription factors (TFs), which have roles in the perception and transduction of stress signals. (biomedcentral.com)
GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. (baderlab.org)
In other cases, different proteins or polypeptides come together to form a functional unit. (jove.com)
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)
In many cases, these genes may also have little or no previous functional characterization. (biomedcentral.com)
BMC Molecular and Cell Biology, formerly known as BMC Cell Biology, is an open access journal that considers articles on all aspects of cellular and molecular biology in both eukaryotic and prokaryotic cells.The journal considers studies on functional cell biology, molecular mechanisms of transcription and translation, biochemistry, as well as research using both the experimental A147 1044-1549 American Journal of Respiratory Cell and Molecular Biology 12.91 144. (spagades.com)
Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology.The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. (spagades.com)
A perspective on the structural and functional constraints INSTRUCTION FOR AUTHORS - SUBMISSION TO ASIA PACIFIC JOURNAL OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY (APJMBB) The Journal aims to promote research in all relevant areas of molecular & cellular biology and biotechnology in the Asia Pacific region through publication of research articles, both basic and applied. (spagades.com)
The human genome encodes 54 functional keratin genes , located in two clusters on chromosomes 12 and 17. (wikipedia.org)
The COPDKB has now been extended to integrate over 40 public data sources on functional interaction (e.g. signal transduction, transcriptional regulation, protein-protein interaction, gene-disease association). (biomedcentral.com)

After analysis of deduced amino acid sequences from cloned cDNAs of dipeptidyl peptidase IV (DPP IV) and aminopeptidase A (APA), it was noticed that DPP IV and APA are type II membrane proteins that have one transmembrane domain near the N-terminus. (nature.com)
The modeling platform developed here uncovers insights into lipid participation in antibodies' recognition of membrane proteins and highlights antibody features to prioritize in vaccine design. (elifesciences.org)
Antibodies can target epitopes on integral membrane proteins very near to the lipid bilayer surface, even those partially embedded within the headgroup region. (elifesciences.org)

To facilitate research on HD in a network-oriented manner, we have developed HDNetDB, a database that integrates molecular interactions with many HD-relevant datasets. (nature.com)
The gene network of ADHD included 599 genes/proteins and 148,978 interactions, while that of dyslexia included 167 genes/proteins and 27,083 interactions. (biomedcentral.com)
However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. (biomedcentral.com)
The Biologically Relevant Analysis of Interaction Networks (BRAIN) is a set of algorithms for predicting and analyzing protein domain-peptide ligand interactions based on experimentally known binding evidence (e.g. from protein chip or phage display experiments). (baderlab.org)
The Signing of Regulatory Networks (SIREN) algorithm can infer the regulatory type (positive or negative regulation) of interactions in a known gene regulatory network given corresponding genome-wide gene expression data. (baderlab.org)
Most of the platforms are expected to be connected to resources for handling various types of user interactions, conceivably with a back-end database management system and a front-end web based technique to handle user interactions. (lu.se)
The GeneRIF (Gene References into Function) directory contains PubMed identifiers for articles describing the function of a single gene or interactions between products of two genes. (nih.gov)
Many biological processes depend on protein-protein interactions. (jove.com)
Similar to ligand binding sites, interactions at a protein-protein interface may involve non-covalent bonds and hydrophobic forces. (jove.com)
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. (jove.com)
Laboratory methods, such as affinity purification, mass spectrometry, and protein microarrays, can be used to identify new interactions. (jove.com)
Computer programs can predict PPIs based on similar interactions found in other proteins by comparing protein sequences and three-dimensional structures. (jove.com)
The field of molecular biology protrudes with biology and chemistry and in particular, genetics and biochemistry and it mainly concerns understanding the interactions Open access options. (spagades.com)

As an example, enrichment of a particular pathway among a list of genes that are differentially expressed after an experimental manipulation may indicate that the pathway has been altered by that manipulation. (univ-lyon1.fr)
We then determined that all three A. marginale genes are modestly differentially expressed in response to altered host cell iron levels, despite the lack of a fur regulator or operon structure. (usda.gov)
Take, for example, the instance where a researcher has identified hundreds or even thousands of differentially expressed genes between a cancer sample and a matched control. (biomedcentral.com)

The BioProject database is a searcheable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects. (nih.gov)
This interface allows the user to search for common OR specific genes/regions between a query genome/replicon and other genomes/replicons chosen from the ones available in our PkGDB database (i.e, (re)annotation of bacterial genomes or complete proteome downloaded from the RefSeq/WGS sections). (cns.fr)
The picture gives an overview of the conservation of synteny groups between the query genome and another genome chosen from the ones available in our PkGDB database (i.e, (re)annotation of bacterial genomes or complete proteome downloaded from the RefSeq/WGS sections). (cns.fr)
The original version of Base-By-Base (BBB) [ 1 ] was developed by the Virus Bioinformatics Resource Center primarily because of a need for a customizable, platform-independent (Java), multiple sequence alignment (MSA) editor that could be used for the comparison, annotation and analysis of viral genomes, and also integrated directly with our MySQL database. (biomedcentral.com)
Epigenetic mechanisms regulating gene expression / John R. McCarrey -- Gene families and evolution / Ben F. Koop -- Repetitive DNA: detection, annotation, and analysis / Jerzy Jurka -- Molecular genetics of disease and the human genome project / Paromita Deb-Rinker and Stephen W. Scherer -- B. Clinical human genetics. (ewubd.edu)
Online gene annotation resources are indispensable for analysis of genomics data. (biomedcentral.com)
Here, we introduce BioGPS http://biogps.gnf.org , a centralized gene portal for aggregating distributed gene annotation resources. (biomedcentral.com)
Dozens of gene annotation resources and model organism databases serve prominent roles in the genetics and genomics communities. (biomedcentral.com)
Each gene annotation resource presents a particular slice of the available gene annotation, generally corresponding to the developers' view of what their users are interested in. (biomedcentral.com)

Cross-referencing with USGENE is possible, with direct links from the well-known genetic sequence database to corresponding PatBase Express records. (piug.org)
Entrez is NCBI's primary text search and retrieval system that integrates the PubMed database of biomedical literature with 38 other literature and molecular databases including DNA and protein sequence, structure, gene, genome, genetic variation and gene expression. (nih.gov)
Typically, designing an experimental piece of DNA containing the gene you're interested in starts with manually going through the actual genetic sequence - thousands of A's, T's, G's, and C's - and, if you were in my lab, using several different colored highlighters to label the important parts on pages in a three-ring binder. (singularityhub.com)
The COPD Knowledge Base is the only publicly available knowledge resource dedicated to COPD and combining genetic information with molecular, physiological and clinical data as well as mathematical modelling. (biomedcentral.com)
Like compounds from biological sources and low-molecular-weight nonoccupational asthma, occupational asthma is probably the chemicals cause occupational asthma after a latent period of result of multiple genetic, environmental, and behavioral exposure. (cdc.gov)

In addition to the sequence databases, you will also learn how to access related information in HomoloGene, UniGene and Gene Expression Omnibus (GEO), how to use precomputed BLAST (BLink) to find homologous proteins and genes, and how to use the Graphical Sequence Viewer as a tool for exploring large and complex genomic sequences and their annotations. (piug.org)
Oftentimes the only way to capture these uncommon sequences is to use the value-added features of the sequence databases on STN. (piug.org)
To ensure accurate molecular epidemiology analyses, we propose a uniform nomenclature for HRSV-positive samples and isolates, and HRSV sequences, namely: HRSV/subgroup identifier/geographic identifier/unique sequence identifier/year of sampling. (cdc.gov)
7 ). The wider availability of viral sequencing technologies has increased submissions of HRSV sequences to databases ( Figure 1 ), a trend we anticipate will continue. (cdc.gov)
Although a poxvirus genome, for example, may be less than 200 kb, it probably encodes close to 200 proteins using multiple classes of promoters with frequent overlapping of promoters and coding sequences and even some overlapping of genes. (biomedcentral.com)
Key distinctive features of the original BBB were its ability to read annotations (CDS positions) from GenBank files, an explicit display of differences between sequences and a tool to compare genomes, including the ability to summarize the consequences of all nucleotide changes on encoded proteins throughout a genome. (biomedcentral.com)
The protein sequences corresponding to the translations of coding sequences (CDS) in GenBank are collected for each GenBank release. (nih.gov)
Icons representing, say, a gene's start and stop sequences, the promoter regions that control when the gene is expressed, or the region that gives bacteria resistance to antibiotics, can be mixed and matched as easily as rearranging apps on an iPad. (singularityhub.com)
Molecular Toolkit - Utilities to analyze and manipulate nucleic acid and protein sequences. (fenteany.com)
siRNA Database - [A] comprehensive siRNA database that contains siRNA targets against all known mRNA sequences throughout a variety of organisms. (fenteany.com)
The availability of multiple PAS in the same 3' regulatory region enables the inclusion or exclusion of 3' untranslated region (3'UTR) sequences, resulting in transcripts that may differ in particularities involving post-transcriptional processes such as stability, transport and translation ( Mayr, 2016 ), and even protein localization ( Berkovits and Mayr, 2015 ). (frontiersin.org)

The collapse of chloroplasts in the necrosis region results in accumulations of polyunsaturated membrane lipids and the lipid-derived phytohormone JA in transgenic lines of Yr36 that encodes Wheat Kinase START 1 (WKS1), a high-temperature-dependent adult plant resistance protein. (bvsalud.org)
Produced by a variety of cell types, extracellular vesicles (EVs) are able to transfer lipids, nucleic acids and proteins to recipient cells. (nature.com)
The founding editors-in-chief were Jerome S. Brody, BBA Molecular and Cell Biology of Lipids publishes papers on original research dealing with novel aspects of lipid biology including the biosynthesis, degrada Journal of cell and molecular biology is a global journal reviewed in the field of bioscience. (spagades.com)

Submissions are encouraged to report on advances in algorithm development and optimization , data structures , data visualization, artificial intelligence/machine learning , text mining , statistical inference, database and ontology development , image analysis , citizen and open science, etc . to analyze all types of biological data. (iscb.org)

In this workshop you will explore the NCBI Entrez integrated biomedical literature and molecular database system and learn how to effectively use the Entrez system to find records of interest. (piug.org)
Given a list of NCBI gene symbols, diffEnrich will perform differential enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. (univ-lyon1.fr)
More detailed help is available for the individual Entrez databases in the NCBI Help Manual sections on the NCBI bookshelf. (nih.gov)
BioProject provides a central point to link to all data associated with a project in the NCBI molecular and literature databases. (nih.gov)
BioSample contains descriptions of biological source materials used in studies that have data in other NCBI molecular databases such as Assembly, Nucleotide and SRA. (nih.gov)
ClinVar provides standardized nomenclature for variants and phenotypes, a review status for variants, and links to related NCBI literature and molecular databases. (nih.gov)
Am069, the A. marginale ortholog of FbpA lacks predicted iron binding residues based on the NCBI conserved domain database. (usda.gov)

KEGG is a database resource for understanding high-level functions of a biological system, such as a cell, an organism and an ecosystem, from genomic and molecular-level information https://www.kegg.jp/kegg/kegg1a.html . (univ-lyon1.fr)
This tool provides some statistics about the similarity results between the selected organism and all the genomes available in our PkGDB database. (cns.fr)
This interface provides an analysis of the pan-genome and its components (core-genome, variable-genome) for an organism set. (cns.fr)
However, writing such summaries is a daunting task, given the number of genes in each organism (e.g. 13,929 protein coding genes in Drosophila melanogaster). (stanford.edu)
The European Ribosomal RNA Database - Ribosomal RNA (rRNA) sequence data listed by organism, secondary structure prediction programs and other software, links to related sites. (fenteany.com)

First, API's, like KEGG's, allow users to perform customized analyses with the most up-to-date versions of the data contained in the database. (univ-lyon1.fr)
RNA-Seq analyses where the background data set includes genes expressed above background). (univ-lyon1.fr)
The resultant subnetwork diagrams from these analyses are useful because this prior knowledge, displayed as a network diagram, contains information about the relationships between the genes identified experimentally. (biomedcentral.com)
The Molecular Biology section is a comprehensive collection of protocols and reviews covering essential and advanced experimental design, methods, and analyses in all areas of molecular biology including the preparation and analysis of DNA, RNA and proteins, sequencing, genome editing, gene regulation and expression, chromatin assembly, and more. (spagades.com)

Molecular genetics: A. Genomics. (ewubd.edu)
Heredity / C.A. Rupar -- The clinical genetics databases / Peter J. Bridge -- Poulation genetics / Jill S. Barnholtz-Sloan. (ewubd.edu)
In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)
The Organizer cordially invites abstracts and full length research papers from all over the World to participate in the World Congress on "Stem Cell Research, Cancer Biology and Applied Biotechnology" (Biotech-2014) is the premier forum for the presentation of new advances and research results in the fields of theoretical, experimental, applied molecular biology, genetics, cell sciences, cancer biology, stem cell research and applied biotechnology. (iranconferences.ir)

Network-based methods can provide valuable tools to consolidate newly generated data with existing knowledge, and to decipher the interwoven molecular mechanisms underlying HD. (nature.com)
The Molecular Mechanisms and Biomarkers Group of the International Agency for Research on Cancer (IARC) is pleased to announce the release of a new version of the IARC TP53 Database. (who.int)
The application of methods of reconstruction and analysis of gene networks is a powerful tool for studying the molecular mechanisms of comorbid conditions. (biomedcentral.com)
Environmental factors that can detect specific IgE antibodies against most low-molecular- affect the initiation of occupational asthma include the intrinsic weight agents has resulted in a search for alternative or characteristics of causative agents as well as the influence of the complementary physiopathologic mechanisms leading to airway level and route of exposure at the workplace. (cdc.gov)

A continuation of MB&B 600a that considers the chemistry and metabolism of nucleic acids, the mechanism and regulation of protein and nucleic acid synthesis, and selected topics in macromolecular biochemistry. (yale.edu)
TOC Part I. Biochemistry, cell, and molecular biology: A. The Cell. (ewubd.edu)
CMS Molecular Biology Resource - Links to resources and tools in molecular biology, biotechnology, molecular evolution, biochemistry and biomolecular modeling. (fenteany.com)
Nigerian Journal of Biochemistry and Molecular Biology (NJBMB) is an international, rigorously peer-reviewed journal, devoted to the advancement of science that is at the interface of chemistry and biology.The purpose of this journal is to provide a medium for the rapid communication of advances and new knowledge in the areas of Biochemistry. (spagades.com)
The American Society for Biochemistry and Molecular Biology helps you excel at all stages of your scientific career through networking, professional development, meetings, journals and leadership opportunities. (spagades.com)

It allows users to obtain, visualize and prioritize molecular interaction networks using HD-relevant gene expression, phenotypic and other types of data obtained from human samples or model organisms. (nature.com)
Human genes altered in IBD have been collected from literature, paying particular interest for the immune system alterations prompted by the interaction with the gut microbiome. (biomedcentral.com)
Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. (biomedcentral.com)
Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect lists of human and mouse genes. (biomedcentral.com)
For instance, a system that we developed a few years ago, Genes2Networks, utilizes twelve protein-protein interaction databases to connect lists of mammalian gene products using a shortest path algorithm [ 1 ]. (biomedcentral.com)
This type of interface is an example of a surface-surface interaction. (jove.com)
This type of interface is known as surface-string interaction. (jove.com)
Another type of interface, known as helix-helix, or coiled-coil interaction, forms when helices of two proteins wrap around each other. (jove.com)
A complex interaction between the cleavage and polyadenylation molecular complex and cis -elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. (frontiersin.org)
Simulations estimating protein-membrane interaction strength for PGZL1 variants along an inferred maturation pathway show bilayer affinity is evolved and correlates with neutralization potency. (elifesciences.org)

The course considers the basic physical chemistry required in cellular and molecular biology but does not require a previous course in physical chemistry. (yale.edu)
The main purpose of a bioinformatics platform within SWEGENE should be to provide com- putational facilities and logistical support [databases & infrastructure] for scientists whose primary research in biology and medicine benefit from computational approaches. (lu.se)
SimGene.com - Molecular biology and bioinformatics tools. (fenteany.com)
The MIT/ICBP siRNA Database - 'The MIT [Massachusetts Institute of Technology]/ICBP [Integrative Cancer Biology Program] siRNA Database is a university-wide effort to catalog these experimentally validated reagents and make that information available to other researchers, both within and outside the MIT community. (fenteany.com)
Read the latest articles of Journal of Molecular Biology at ScienceDirect.com, Elseviers leading platform of peer-reviewed scholarly literature Forum. (spagades.com)
Official site of the Journal of Molecular Biology. (spagades.com)
Cellular and Molecular Biology publishes original articles, reviews, short communications, methods, meta-analysis notes, letters to editor and comments in the interdisciplinary science of I will recommend this book to all my colleagues. (spagades.com)
Current Issues in Molecular Biology. (spagades.com)
This journal has merged with BMC Molecular and Cell Biology. (spagades.com)
American Journal of Molecular Biology SCIAMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY Reliably documenting plant diversity is necessary to protect and sustainably benefit from it. (spagades.com)
Journal of Molecular Biology citation style guide with bibliography and in-text referencing examples: Journal articles Books Book chapters Reports Web pages. (spagades.com)

Additionally, it was revealed that the most relevant genes are involved in biological processes related to signal transduction, positive regulation of transcription from RNA polymerase II promoters, chemical synaptic transmission, response to drugs, ion transmembrane transport, nervous system development, cell adhesion, and neuron migration. (biomedcentral.com)
This approach also abstracts the genes from the query list to higher order biological functions, allowing for the identification of novel relevant genes. (biomedcentral.com)
All the venomous species have a venom gland that synthesizes, stores and secretes a complex mixture of biological molecules including proteins. (nature.com)
This initiative is one of the integrated components of the NIH Molecular Libraries Roadmap initiative that offers biomedical researchers access to large-scale automated high throughput screening (HTS) centers in the MLPCN, diverse compound libraries in the Small Molecule Repository (MLSMR) and information on biological activities of small molecules in the PubChem BioAssay public database. (nih.gov)
7. Molecular Cell is particularly interested in papers that answer longstanding questions, open new avenues of research, report unexpected findings, or change the way we think about biological processes. (spagades.com)

This document is an overview of the Entrez databases, with general information on searching and displaying data. (nih.gov)
The Entrez search interface features powerful options for constructing precise searches and managing results. (nih.gov)
Most importantly Entrez integrates data with links within and between databases. (nih.gov)
The Entrez system comprises 39 molecular and literature databases. (nih.gov)
The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. (biomedcentral.com)
Each site often accepts a different set of gene identifiers (Entrez Gene, Ensembl, Refseq, Unigene, and so on), making it difficult for users to find their gene of interest. (biomedcentral.com)

This site contains the full taxonomy database along with files associating nucleotide and protein sequence records with their taxonomy IDs. (nih.gov)
This site contains all nucleotide and protein sequence records in the Reference Sequence (RefSeq) collection. (nih.gov)
FASTA - 'Provides sequence similarity searching against nucleotide and protein databases using the Fasta programs. (fenteany.com)

However, in protein modification studies, the typical experimental design compares the presence or absence of particular modified proteins between multiple groups. (univ-lyon1.fr)
Various software resources are also required to enable users to conveniently connect their experimental results with publicly, and application specific, bioinformatics databases and tools. (lu.se)
Previously we generated a chronic obstructive pulmonary disease (COPD) specific knowledge base ( http://www.copdknowledgebase.eu ) from clinical and experimental data, text-mining results and public databases. (biomedcentral.com)
This knowledge base allowed the retrieval of specific molecular networks together with integrated clinical and experimental data. (biomedcentral.com)

It is a critical component of eukaryotic and prokaryotic cellular functions and is indispensable for nucleic acid synthesis, protein production, and energy generation. (usda.gov)
This interface is observed frequently in proteins that contain leucine zipper domains such as eukaryotic transcription factors. (jove.com)
In addition, after transcription, a wide array of RNA-binding proteins interacts with cis -acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. (frontiersin.org)

You will understand the scope and content of the sequence databases (Nucleotide, GSS, EST, Protein and SRA). (piug.org)
Conserved Domains is a database of protein domains represented by sequence alignments and profiles for protein domains conserved in molecular evolution. (nih.gov)
We have endeavoured to make the tool intuitive and to add features that are useful to molecular biologists working daily with large viral genomes (up to 300 kb) that contain approximately 1 gene/kb of sequence. (biomedcentral.com)
Pattern discovery: methods and software / Brona Brejova, Tomas Vinar, and Ming Li -- The role of transcription factor binding sites in promoters and their In Silico detection / Thomas Werner -- An introduction to multiple sequence alignment and analysis / Steven M. Thompson -- 3D molecular visualization with protein explorer / Eric Martz -- Multiple sequence alignment and analysis: the Seqlab interface: a practical guide / Steven M. Thompson -- D. Analysis of gene expression: microarrays and other tools. (ewubd.edu)
LOLA (LOgos Look Amazing) is a tool for generating sequence logos using Position Weight Matrix based protein profiles. (baderlab.org)
Sequence databases for use with the stand-alone BLAST programs. (nih.gov)
Sequence databases in FASTA format for use with the stand-alone BLAST programs. (nih.gov)
ClustalW - '[A] general purpose multiple sequence alignment program for DNA or proteins. (fenteany.com)

For instance, many enzymes, such as protein kinase A here, form a cleft that can recognize and bind polypeptide loops of their binding partners. (jove.com)

EBI Services - Access to nucleic acid, protein and macromolecular structure databases, including the EMBL-Bank database. (fenteany.com)

The resource provides a section devoted to human genes identified as altered in IBD, which can be queried at different biomolecular levels and visualised in gene-centred report pages. (biomedcentral.com)
The IBDsite is an attempt to group available information regarding human genes and microbial aspects related to IBD, by means of a multilevel mining tool. (biomedcentral.com)
BodyMap - An anatomical expression database of human genes. (fenteany.com)

We lack tools to prevent these diseases in part due to major knowledge gaps in our basic understanding of the tick-pathogen interface, including the requirement for and molecules involved in iron transport during tick colonization. (usda.gov)
It is capable of working with protein and DNA molecules, but many of its unique features relate to the manipulation of the genomes of large DNA viruses such as poxviruses, herpesviruses, baculoviruses and asfarviruses (1-400 kb). (biomedcentral.com)
Although senataxin's role in cells is not completely understood, it appears to be involved in the production of proteins from genes (transcription), the processing of RNA molecules, and the repair of damaged DNA. (medlineplus.gov)

For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. (scienceopen.com)

This interface allows the user to define a set of genomes and displays a tree showing the genomic similarity. (cns.fr)
The RGP_Finder method first starts with the identification of synteny breaks between a query genome and other close genomes chosen from the ones available in our PkGDB database. (cns.fr)
These events are computed from the synteny results obtained with the genomes available in the PkGDB database. (cns.fr)
Among the computed values between two compared genomes are: the number and percentage of genes which are in BBH (Bidirectional Best Hit) and in synteny groups, the synteny groups number and size, etc. (cns.fr)
Genomes OnLine Database - 'GOLD: Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world. (fenteany.com)

For instance, he and his friends are already creating a database for expression tags to be placed on different proteins. (singularityhub.com)

In order to identify genes that may modify disease onset and progression, genome-wide association and gene expression studies have been performed 12 , 13 . (nature.com)
The availability of pearl millet transcriptome and genome data helps to identify genes that contribute to stress tolerance in pearl millet. (biomedcentral.com)

Through APA, a single gene containing multiple PAS can generate a considerable number of transcript isoforms, thereby producing a highly diversified transcriptome ( Tian and Manley, 2013 ). (frontiersin.org)

Co-immunoprecipitation of proteins and yeast two-hybrid screening are widely used to provide evidence on whether two proteins interact in vitro . (jove.com)

Using bioinformatics and protein modeling we identified orthologs of the Gram-Negative siderophone-independent iron uptake system, FbpABC. (usda.gov)
Nucleic acids and proteins: modern linguistics for the genomics and bioinformatics era / Bradley C. Hyman -- Structure and function of cell organelles / Jon Holy -- Cell signaling / Daniel A. Rappolee -- B. Transcription and translatio. (ewubd.edu)
The purpose of a bioinformatics platform within SWEGENE is to provide computational facilities and logistical support [databases, algorithms & infrastructure] for problem oriented scientists in an optimal way. (lu.se)

This interface allows the user to search for potentially horizontally transferred genes (HGT) which are gathered in genomic regions (Region of Genomic Plasticity). (cns.fr)

The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. (biomedcentral.com)

You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. (baderlab.org)

The approach is based on ten criteria for ranking genes by their importance, including relevance scores of association between disease and genes, standard methods of gene prioritization, as well as original criteria that take into account the characteristics of an associative gene network and the presence of known polymorphisms in the analyzed genes. (biomedcentral.com)
Various computational and biochemical methods are used to study protein interfaces. (jove.com)

We address the feasibility and determinant molecular features of this mechanism using integrative modeling. (elifesciences.org)

Overview of the tools for microarray analysis: transcription profiling, DNA chips, and differential display / Jeffrey A. Kramer -- Microarays: tools for gene expression analysis / Sorin Draghici -- Knowledge discovery from the human transcriptome / Kousaku Okubo and Teruyoshi Hishiki.l. (ewubd.edu)
Our genome-wide analysis found 151 NAC transcription factor genes ( PgNAC s) in the pearl millet genome. (biomedcentral.com)
The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. (biomedcentral.com)
Groh M, Albulescu LO, Cristini A, Gromak N. Senataxin: Genome Guardian at the Interface of Transcription and Neurodegeneration. (medlineplus.gov)

The 3' regulatory regions have a great diversity of cis -regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. (frontiersin.org)
Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. (frontiersin.org)
In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions. (frontiersin.org)

Molecular biotechnology has made it possible to explore the potential of plants for different purposes. (frontiersin.org)

However, based on protein modeling, the best structural orthologs of Am069 are iron transport proteins from Cyanobacteria and Campylobacter jejuni. (usda.gov)
Keratin ( / ˈ k ɛr ə t ɪ n / [1] [2] ) is one of a family of structural fibrous proteins also known as scleroproteins . (wikipedia.org)

Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast. (mbl.edu)

GOBASE - The Organelle Genome Database - 'GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. (fenteany.com)

You will also explore aspects of the literature databases (PubMed and PubMed Central) with emphasis on the linkages between the literature and molecular data. (piug.org)
The most appropriate background data set would be proteins present in that tissue, but this would require a separate analytical analysis. (univ-lyon1.fr)
New databases are added as biomedical science advances and new kinds of data become available. (nih.gov)
The IARC TP53 Database is a molecular epidemiology resource that compiles TP53 gene variations identified in human populations and tumour samples, with associated data on tumour pathology and patient characteristics. (who.int)
When the ANDSystem and GeneCards data were combined, a total of 213 genes/proteins for ADHD and dyslexia were found. (biomedcentral.com)
A user-friendly web interface has been created for easy access to structured data. (biomedcentral.com)
Tools such as gene clustering coefficients, all-pairs shortest paths and pathway lengths calculation have been developed to provide data analysis support. (biomedcentral.com)
An in-house algorithm predicts and ranks expert authors for each gene based on the data within FlyBase and extracts their email addresses from papers that we have curated. (stanford.edu)
We discuss the general utility of this approach for other databases that capture data from the research literature. (stanford.edu)
Web Application Programming Interfaces (APIs) are interfaces that data providers build to empower the outside world to interact with their business logic. (stanford.edu)
The DATA directory contains files listing all data linked to GeneIDs along with subdirectories containing ASN.1 data for the Gene records. (nih.gov)
Sample programs for manipulating gene data are provided in the tools directory. (nih.gov)
This site provides data from the PubChem Substance, Compound and Bioassay databases for download via ftp. (nih.gov)
The data derived from these high-throughput approaches can then be used to generate new hypotheses or inferences of gene function. (biomedcentral.com)
Update existing and integrate further COPD-specific knowledge and semantically map it to clinical, physiological and molecular data of COPD patients to generate a full repository of COPD-associated features. (biomedcentral.com)

KEGG is an integrated database resource consisting of eighteen databases that are clustered into 4 main categories: 1) systems information (e.g. hierarchies and maps), 2) genomic information (e.g. genes and proteins), 3) chemical information (e.g. biochemical reactions), and 4) health information (e.g. human disease and drugs) https://www.kegg.jp/kegg/kegg1a.html . (univ-lyon1.fr)

2004). Specificity is determined using BLAST against UniGene databases. (fenteany.com)

Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. (biomedcentral.com)

The large number of genes and the diversity of processes involved in the progression of neurological diseases in general, and HD in specific, emphasizes the need for comprehensive approaches in additional to studies of individual genes 14 . (nature.com)
An approach for ranking genes implicated in the comorbid condition of the two diseases was proposed. (biomedcentral.com)
According to the proposed approach, the genes OPRM1, CHRNA4 and SNCA had the highest priority in the development of comorbidity of these two diseases. (biomedcentral.com)
We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. (biomedcentral.com)
Our finding that disease genes in many cancers are mostly connected through PPIs whereas other complex diseases, such as autism and type-2 diabetes, are mostly connected through FANs without PPIs, can guide better strategies for disease gene discovery. (biomedcentral.com)
It provides unique identifiers, names and synonyms, list of complex members with their unique identifiers (UniProt, ChEBI, RNAcentral), function, binding and stoichiometry annotations, descriptions of their topology, assembly structure, ligands and associated diseases as well as cross-references to the same complex in other databases (e.g. (stanford.edu)
In addition graph based navigation allowed single step network expansions to e.g. navigate from a group of patients to the diseases they are diagnosed with and from there to the genes associated with these diseases. (biomedcentral.com)

It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. (nih.gov)
Often researchers want to go beyond the network of proteins or genes and also look at the inter-connectedness between colleagues and institutions. (baderlab.org)
User interfaces vary dramatically, and researchers must learn and remember how to navigate each site. (biomedcentral.com)
For example, researchers routinely mutate amino acids to histidines which can then act as a marker to locate, purify and quantify that protein. (singularityhub.com)
A critiquable database where researchers can submit their 'cheat sheets' of what works best could be a time-saving alternative to searching the literature. (singularityhub.com)
However, validation with user groups showed that to enable application by clinical researchers, a significant simplification of the user interface was required. (biomedcentral.com)
Based on the structure of senataxin, researchers believe that it is one of a class of proteins called helicases, which attach to particular regions of DNA or RNA (a chemical cousin of DNA) and temporarily unwind the strands of the molecule. (medlineplus.gov)

Human HTT codes for a large protein of 3144 amino acids, which is ubiquitously expressed in various tissues and is present in several sub-cellular locations. (nature.com)
However, covalent disulfide bonds between cysteine amino acids on each protein surface may also play a role to keep them together. (jove.com)
Most mutations replace single protein building blocks (amino acids) in senataxin. (medlineplus.gov)

Eukaryotes have a mechanism termed alternative polyadenylation (APA), which allows the selective use of PAS in genes containing multiple PAS. (frontiersin.org)

Brief summaries describing the function of each gene's product are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. (stanford.edu)
Ancillary protein-lipid contacts reveal surprising contributions from antibody framework regions. (elifesciences.org)

These proteins are responsible for inducing several pharmacological effects aiming to immobilize and initiate the pre-digestion of the prey. (nature.com)

Anatomy4

Organisms3

Diseases2

Chemicals and Drugs30

Analytical, Diagnostic and Therapeutic Techniques and Equipment56

Psychiatry and Psychology2

Phenomena and Processes65

Disciplines and Occupations15

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture12

Information Science87

Health Care28

Geographicals2

Pathways14

Candidate genes12

Functional22

Membrane proteins3

Interactions13

Differentially expressed3

Annotation9

Genetic5

Sequences11

Lipids3

Ontology1

NCBI7

Organism5

Analyses4

Genetics4

Mechanisms4

Biochemistry5

Interaction10

Biology11

Biological5

Entrez6

Nucleotide and protein3

Experimental4

Eukaryotic3

Sequence8

Enzymes1

Macromolecular1

Human genes3

Molecules3

Experimentally1

Genomes5

Different proteins1

Identify genes2

Single gene1

Yeast1

Bioinformatics3

Genomic regions1

Mammalian gene1

Kinases1

Methods2

Integrative1

Transcription4

Regulatory3

Biotechnology1

Structural2

RRNA1

Genome database1

Data15

Biochemical1

UniGene1

Similarity1

Diseases7

Researchers7

Amino3

Mechanism1

Reveal2

Pharmacological1