Genome annotations genome gene databases protein. Medical search. Frequent questions

KEGG) database, Cluster of Orthologous Groups of proteins (COG), Gene Ontology (GO), and protein families (Pfam). (cdc.gov)
and (e) curate functional and structural annotations (gene ontology, enzymatic functions, protein structure). (usda.gov)
Gene Ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). (hindawi.com)
In our approach, annotation was provided through Gene Ontology terms by applying multiple Support Vector Machines (SVM) for the classification of correct and false predictions. (biomedcentral.com)
We present a complete automated annotation system that overcomes many of the usual problems by applying a controlled vocabulary of Gene Ontology and an established classification method on large and well-described sequence data sets. (biomedcentral.com)
Gene ontology functional enrichment analysis was performed using search tool for the retrieval of interacting genes/proteins. (ijpsonline.com)
Gene ontology functional enrichment analysis revealed twenty eight biological processes and 10 molecular functions associated with cognitive impairment. (ijpsonline.com)
To increase our understanding of these differentially expressed unigenes, we performed Gene ontology and KEGG pathway enrichment analyses. (biomedcentral.com)
The signature mechanism was studied by analyzing the gene ontology and the Kyoto Encyclopedia of Genes and Genome database. (peerj.com)
BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. (sri.com)
He has contributed significantly to the state-of-the-art by frequently presenting novel ideas, methods and results and have pioneered several important proof-of-concepts relevant for the project, including the conceptualization of DNA, RNA and protein variation to Variation Ontology (Vihinen, Genome Res . (lu.se)
Whole genome analysis of lung, sampled 24 hours after challenge, showed expression changes of not only genes belonging to several Gene Ontology groups with up-regulation of inflammatory-associated genes and those associated with lung remodeling but also genes involved in downsizing these processes. (cdc.gov)

The gene sequences were downloaded from the NCBI. (cdc.gov)
In spite of their broad abundance, viruses, in particular bacteriophages, remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be annotated by comparison with public databases. (mdpi.com)
We applied our trained classification system to Xenopus laevis sequences, yielding functional annotation for more than half of the known expressed genome. (biomedcentral.com)
In a case study, the function for Xenopus laevis contig sequences was predicted and the results are publicly available at ftp://genome.dkfz-heidelberg.de/pub/agd/gene_association.agd_Xenopus . (biomedcentral.com)
Accurate annotation has traditionally been maintained manually with the experience of individual experts and the experimental characterisation of sequences. (biomedcentral.com)
This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. (lu.se)
Scan several protein sequences or a whole genome (all ORFs) against HAMAP family profiles. (expasy.org)
Sequences that match HAMAP profiles will be annotated in the UniProtKB format by the associated annotation rules. (expasy.org)
Genome sequences of 358 bacterial cultures have been determined with WGS. (biomedcentral.com)
Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. (stanford.edu)
Sorcerer II is expected to more than double the number of protein sequences currently available in the National Institutes of Health's GenBank. (jcvi.org)
The metagenomics database will include new sequences, genes and gene families, together with their annotations and associated environmental metadata. (jcvi.org)
eggNOG-mapper is a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed eggNOG clusters and phylogenies. (cns.fr)
As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. (sri.com)
Since biochemistry and genetics have not, by and large, enjoyed the same improvement of scale, public sequence repositories now predominantly contain putative protein sequences for which there is no direct experimental evidence of function. (plos.org)

We performed AST and whole genome sequencing (WGS) for 593 C. difficile isolates collected between 2012-2017 through the Centers for Disease Control and Prevention's Emerging Infections Program. (cdc.gov)
Whole-Genome Sequencing Reveals Diversity of Carbapenem-Resistant Pseudomonas aeruginosa Collected through CDC's Emerging Infections Program, United States, 2016-2018. (cdc.gov)
To characterize the pathotype, 1,019 isolates collected through this project underwent antimicrobial susceptibility testing and whole-genome sequencing. (cdc.gov)
To contribute to the hazard identification of low molecular weight (LMW) respiratory allergens, respiratory allergy induced by trimellitic anhydride (TMA) was characterized by whole genome analysis of lung tissue and blood proteomics in Brown Norway rats. (cdc.gov)

The pathways that are probably regulated by the identified plant phytoconstituents were analyzed using Kyoto encyclopedia of genes and genomes. (ijpsonline.com)
Kyoto encyclopedia of genes and genomes pathway identified eight pathways that are directly related to cognitive impairment. (ijpsonline.com)

This study examines the gene expression of 33 fatty acid-related genes when the cyanobacterium Chlorogloeopsis fritschii PCC 6912 is grown under far-red light compared to white light using RNA-seq data from the NCBI database. (exeter.ac.uk)
This tool provides some statistics about the similarity results between the selected organism and all the bacterial genomes available in RefSeq/WGS NCBI sections. (cns.fr)

Predicted CDS were compared to the databases InterPro ( 18 ), Swissprot ( 19 ), and trEMBL ( 19 ) for functional annotation and mapped to KEGG pathways. (asm.org)

How many protein-coding genes in the human genome? (blogspot.com)
It's difficult to know how many protein-coding genes there are in the human genome because there are several different ways of counting and the counts depend on what criteria are used to identify a gene. (blogspot.com)
Those authors discussed the problems with annotation and pointed out that the major databases don't agree on the number of gene [ How many protein-coding genes in the human genome? ]. (blogspot.com)
The human genome encodes ∼20,000 proteins, many still uncharacterised. (biorxiv.org)
Since the release of the first draft of the human genome sequence in 2000, the function of many of these new proteins has been identified. (biorxiv.org)

What pathways are this gene/protein implicaed in? (cancerindex.org)
Gene regulation in fatty acid pathways in cyanobacteria exposed to far-red light. (exeter.ac.uk)
Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
We further identified changes in module eigenproteins indicative of dysregulation in protein translation and trafficking pathways. (stanford.edu)
Mauno Vihinen is well-known for his experience and interest in investigating variations and their effects whether they emerge at molecular levels (DNA, RNA protein), in structural context or in the cellular networks and pathways. (lu.se)
Unsensitized animals challenged with TMA exhibited also an increased number of macrophages in BAL, but gene expression in the above-mentioned gene pathways was unchanged or down-regulated. (cdc.gov)

LC-MS/MS and bioinformatics analysis were performed to identify differentially expressed proteins. (frontiersin.org)
Bioinformatics analysis indicated the up-regulated proteins were significantly enriched in "GnRH secretion" and "Circadian rhythm" signaling pathway. (frontiersin.org)
Bioinformatics data mining of gene expression profiles using the Gene Expression Omnibus (GEO) database has led to identifying promising biomarkers associated with disease development [ 12 ]. (hindawi.com)
See also our pages on BioInformatics and on the Trypanosoma cruzi Genome Initiative. (fiocruz.br)
In this research, we conducted a multi-step analysis through comprehensive bioinformatics analysis to identify hub genes in THCA. (peerj.com)
Lee T.J., Pouliot Y., Wagner V., Gupta P., Stringer-Calvert D.W.J, Tenenbaum J.D., Karp P.D. BioWarehouse: a bioinformatics database warehouse toolkit. (sri.com)
This article addresses the problem of interoperation of heterogeneous bioinformatics databases. (sri.com)
We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. (sri.com)
BioWarehouse embodies significant progress on the database integration problem for bioinformatics. (sri.com)
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)
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)
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)

The model on this page is part of a hierarchical collection of curated Hidden Markov Model-based and BLAST-based protein families (HMMs and BlastRules), and Conserved Domain Database architectures used to assign names, gene symbols, publications and EC numbers to the prokaryotic RefSeq proteins that meet the criteria for inclusion in a family. (nih.gov)
The number of RefSeq proteins with identity and coverage above the BlastRule's identity and coverage cutoffs, respectively. (nih.gov)
No RefSeq protein is named by this evidence. (nih.gov)
All matching RefSeq proteins are named by this evidence. (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 validation results show that the prediction performance was organism-independent and could reproduce the annotation of other automated systems as well as high-quality manual annotations. (biomedcentral.com)
To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
The move from traditional organism genome databases to the CAMERA-based environmental metagenomics data storage and computational complex requires development of a more complex cyber-architecture. (jcvi.org)
To find the homologs, the tool analyses the similarity results between the genes of each organism and the set of 206 genes from 7 genomes (Escherichia coli K12, Bacillus subtilis 168, Candidatus Blochmania floridanus, Buchnera aphidicola APS, Buchnera aphidicola Bp, Buchnera aphidicola Sg and Mycoplasma genitalium G37). (cns.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)

Objective 2: Develop computational and visualization tools to curate, integrate, and query the genetic, genomic, and phenotypic relationships in small grains germplasm, and deploy machine learning and artificial intelligence approaches to enhance functional annotations and discover biological interactions. (usda.gov)
The Expedition is developing the first large-scale genomic survey of microbial life in the world's oceans to produce the largest gene catalogue ever assembled. (jcvi.org)
This functionalty provides the list of Genomic regions containg tandem duplications of protein coding genes. (cns.fr)
This interface allows the user to define a set of genomes and displays a tree showing the genomic similarity. (cns.fr)
The genomic similarity is estimated using Mash , a software that computes a distance between two genomes. (cns.fr)
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)
Prior to the "genomic era," when the acquisition of DNA sequence involved significant labor and expense, the sequencing of genes was strongly linked to the experimental characterization of their products. (plos.org)
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland. (who.int)

Two transcript variants encoding different isoforms have been found for this gene. (nih.gov)
Common variants in AGR1 genes contributed to the risk and traits of cirrhotic cardiomyopathy in the Han Chinese population. (nih.gov)
Variants in blood pressure genes and the risk of Accardi R, Rubino R, Scalise M et col . (2011). (who.int)

These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. (sri.com)
More recently, a genome-scale metabolic network model of Synechocystis sp. (biomedcentral.com)
Collectively, our data indicate that MSC therapy rescues impaired mitochondrial morphology, enhances host metabolic capacity, and induces widespread host gene shifting. (frontiersin.org)

This set of known sequence-function relationships will ultimately serve as the basis for making predictions for similar proteins whose functions have not been experimentally determined and can be used to train other types of prediction-generating algorithms. (plos.org)

The R package was used for data mining and screening differentially expressed genes (DEGs). (hindawi.com)
In this study, a data mining strategy was used to obtain 2 microarray datasets of gastric cancer from the GEO database to identify differentially expressed genes (DEGs) associated with gastric cancer occurrence and progression. (hindawi.com)
The GSE3467 , GSE3678 , GSE33630 and GSE53157 were obtained from the GEO database, including 100 thyroid tumors and 64 normal tissues to obtain the intersection of differentially expressed genes, and a protein-protein interaction network was constructed to obtain the HUB gene. (peerj.com)
With the development of RNA sequencing and microarray technology, the study of differentially expressed genes (DEGs) between cancer and normal tissues has improved our understanding of the molecular mechanism of PTC. (peerj.com)

This work describes the complete genome sequence of this phage. (biomedcentral.com)
This work focuses on the determination of the complete genome sequence of the P. fluorescens phage ϕIBB-PF7A. (biomedcentral.com)

The ICE1-CBF-COR transcriptional cascade (inducer of CBF expression 1 and C-repeat binding factor transcriptional cascade) is the best characterized pathway for gene regulation under cold conditions in many species [ 8 ]. (biomedcentral.com)
Using GSEA analysis, we found that the antigen processing and presentation pathway were related to the five tumor coexpressed genes mentioned above. (hindawi.com)

Also, expression verification and survival analysis of these candidate genes based on the TCGA database indicate the robustness of the above results. (peerj.com)
This tool provides a list of candidate genes of a query genome potentially involved in a fusion or a fission event. (cns.fr)

A combination of de novo transcriptome assembly and DGE analysis was shown to be a powerful method for identifying genes encoding enzymes potentially involved in the biosynthesis of important secondary metabolites in a non-model plant. (biomedcentral.com)

HMMs and BlastRules also contribute to structural annotation by NCBI's Prokaryotic Genome Annotation Pipeline ( PGAP ) ( Read more ). (nih.gov)

Sequenced genomes were classified using the seven-gene multilocus sequence typing (MLST) scheme and a core genome (cg)MLST scheme was used to determine phylogeny. (cdc.gov)

Compared to the currently available annotation, we provided more than twice the number of contigs with good quality annotation, and additionally we assigned a confidence value to each predicted GO term. (biomedcentral.com)
The following tables give some information about the replicons of the genome such as: Length, GC%, Ribosomal RNAs, tRNAs types, Annotations Status, Average CDS length, Repeated regions, Average intergenic length, Protein coding density, number of contigs/scaffolds etc. (cns.fr)

Genotyping of ASFV isolates by partial sequencing of the B646L gene that encodes the major capsid protein p72 has identified 22 genotypes ( 6 ). (cdc.gov)

WGS was performed on all isolates to detect the presence of genes or mutations previously associated with resistance. (cdc.gov)
RT027 isolates also showed higher MICs to clindamycin and moxifloxacin and were more likely to harbor associated resistance genes or mutations. (cdc.gov)
While only 7 (0.1%) isolates harbored carbapenemase genes, 66 (6.5%) had acquired non-carbapenemase -lactamase genes, and these were more likely to have OprD dysfunction and be resistant to all carbapenems tested. (cdc.gov)
The increased carbapenem resistance in isolates with acquired non-carbapenemase -lactamase genes suggests that horizontally transmitted mechanisms aside from carbapenemases themselves may be important drivers of the spread of carbapenem resistance in P. aeruginosa. (cdc.gov)
Previous data for sequencing of 3 genes indicated that the Georgia 2007/1 isolate is closely related to isolates of genotype II, which has been identified in Mozambique, Madagascar, and Zambia. (cdc.gov)
90,000 animals died or were destroyed (www.oie.int). Experimental infections of pigs confirmed that isolates obtained after introduction of ASF into Armenia and the Russian Federation cause acute disease and result in high mortality rates (www.efsa.europa.eu/en/scdocs/scdoc/1556.htm). (cdc.gov)

The CAMERA project builds on pioneering efforts in metagenomics to sequence the genomes of entire microbial communities, often comprising thousands of species. (jcvi.org)

Today, phage genome sequencing is commonly performed for classification and characterization purposes and is based on the arrangement of conserved genes and the nucleotide and protein sequence identity [ 5 , 6 ]. (biomedcentral.com)

Commonly, computational functional assignment is based on homologues identified from database searches [ 5 ]. (biomedcentral.com)
Computational approaches attempt to leverage evidence associated with the ever-smaller fraction of experimentally analyzed proteins to predict function for these putative proteins. (plos.org)
Maximizing our understanding of function over the universe of proteins in toto requires not only robust computational methods of inference but also a judicious allocation of experimental resources, focusing on proteins whose experimental characterization will maximize the number and accuracy of follow-on predictions. (plos.org)
COMBREX ( COM putational BR idges to EX periments, http://combrex.bu.edu ) is an NIH-funded enterprise that has brought computational and experimental biologists together, with the goal of greatly improving our overall understanding of microbial protein function [1] , [2] . (plos.org)

2018) that concluded there were somewhere between 19,000 and 20,000 protein-coding genes. (blogspot.com)

The transcriptomic analysis, encompassing a bioinformatic pipeline to process and quantify transcripts, found that only two genes of the 33 examined genes were differentially expressed. (exeter.ac.uk)
eggNOG pipeline is the clustering of the 9.6 million proteins from 2031 genomes. (cns.fr)

Gene Indices (EST analyses) at TIGR. (fiocruz.br)
Emma Lundberg's group has a wealth of experience in using microscopy to yield biological images that paint a picture of this cell-to-cell heterogeneity of protein expression information, and joining her lab has deepened my expertise in integrating datasets to perform innovative analyses of single-cell protein expression. (stanford.edu)
He has published numerous original ideas and reports, established standards and guidelines for variations and variation databases and developed tools and performed analyses for the interpretation of variations in several diseases. (lu.se)

While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. (nature.com)
In this context, the exploration of temporal interplay between populations with different lifestyles (comprising metabolism, motility, sporulation, etc.) becomes of primary importance to interpret the changes in fundamental quantities in a microbial community, such as the protein-to-RNA ratio that ultimately impacts the overarching community phenotype(s). (nature.com)
In order to perform studies of such design and test if previously defined quantitative data about the functioning of microorganisms (i.e., protein-to-RNA ratio) is applicable to real world consortia, we must first sample microbial communities across transition events and employ quantification techniques that are absolute. (nature.com)
Second, the project maintains a web-accessible database (the COMBREX Database ) of known and predicted functions for microbial proteins. (plos.org)

We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. (asm.org)

This gene is a member of the protein-tyrosine kinase oncogene family. (cancerindex.org)
The protein associates with the p85 subunit of phosphatidylinositol 3-kinase and interacts with the fyn-binding protein. (cancerindex.org)
AICAR is an adenosine analog that selectively activates AMP-activated protein kinase (AMPK). (stemcell.com)
May be a target of DMI3, a calcium/calmodulin-dependent protein kinase (CCaMK) (PubMed:15961669). (gao-lab.org)

The GO terms are organised in structured, controlled vocabularies (ontologies) to describe gene products in terms of their associated biological processes, cellular components and molecular functions. (biomedcentral.com)
This study also highlights the need for greater biological replicates within RNA-seq experiments and increased completeness in genome annotations in biotechnological databases. (exeter.ac.uk)
We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scientific community. (lu.se)
. pilosum and a de novo assembled transcriptome, which can be used to characterize genes related to diverse biological processes. (biomedcentral.com)
The mystery and the potential biological significance of these unknown genes is enhanced by many of them being well conserved, and many of them being completely unrelated to known proteins and thus lacking clues to their function. (biorxiv.org)
The recommendation system is a proof of concept based on active learning principles and includes, for a given protein, criteria including phylogenetic distribution of its protein family, biological and clinical phenotypes associated with it, the availability of protein structure data, and its sequence distance from experimentally determined proteins or from the other proteins in its family. (plos.org)

The gastric cancer microarray dataset was downloaded from the Gene Expression Omnibus (GEO) database. (hindawi.com)
Furthermore, microarray profiling identified 226 genes with differential expression in the liver of animals treated with MSC, with cellular signaling, and actin cytoskeleton regulation as key upregulated processes. (frontiersin.org)

Here we report the temporal measurements of absolute RNA and protein levels per gene within a mixed bacterial-archaeal consortium. (nature.com)
Our analysis of this data reveals an absolute protein-to-RNA ratio of 10 2 -10 4 for bacterial populations and 10 3 -10 5 for an archaeon, which is more comparable to Eukaryotic representatives' humans and yeast. (nature.com)
Indeed, the protein-to-RNA ratio per sample of the bacterial populations matched previous calculations for the existing example from axenically cultured E. coli 2 . (nature.com)
Gil R, Silva FJ, Peret J, «Moya A. Determination of the core of a minimal bacterial gene set. (cns.fr)
This tool draws a global comparison, based on synteny results (the size of which can be selected by the user) between 2 bacterial genomes. (cns.fr)

The two genes were down-regulated and encoded for a fatty acid desaturase (fad) and a pfaD/polyketide biosynthesis protein. (exeter.ac.uk)
Ethanol can interfere with cell membrane's ability to act as a barrier, and interrupt key cellular processes such as protein biosynthesis, energy transduction and transport[ 8 ]. (biomedcentral.com)

The phylogenetic analysis of the strain was based on 16S rRNA gene sequencing and showed that Paenibacillus sp. (asm.org)
Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. (lu.se)

CRISPRdigger was used to predict the CRISPRs (clustered regularly interspaced short palindromic repeats) of the genome. (cdc.gov)
To do this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information, and used all annotated and predicted proteins to identify potential protein domains. (mdpi.com)
There have been initiatives to develop new means to predict protein function or structure ( 9 - 13 ). (biorxiv.org)
From a partitioned genome, it applies a score-based algorithm to predict RGPs (>3kbp). (cns.fr)

Scope includes mutations and abnormal protein expression. (cancerindex.org)
The lack of vanA/B genes or mutations consistently associated with elevated vancomycin MICs suggests there are multifactorial mechanisms of resistance. (cdc.gov)
Mutations associated with dysfunction of the porin OprD were found in 888 (87.1%) of the genomes and were correlated with carbapenem resistance, and a machine learning model incorporating hundreds of genetic variations among the chromosomal mechanisms of resistance was able to classify resistant genomes. (cdc.gov)
It is a subset of the dataset available in Database of Curated Mutations (DoCM) . (lu.se)
The database of Cancer Passenger Mutations (dbCPM) for curated passenger variations that are unlikely to engage in cancer development, progression, or therapy. (lu.se)
DoCM: a database of curated mutations in cancer. (lu.se)

. pilosum, none of the identified cold responsive (COR) gene orthologs was induced by cold, which is consistent with the lack of cold tolerance in this plant. (biomedcentral.com)

Circular genome maps were generated using Circos (Version 0.64) based on analysis of the coverage of sample sequencing reads, single-nucleotide polymorphisms (SNPs), and InDels. (cdc.gov)
This report represents the first description of combined label-free quantitative proteomics and PRM analysis of targeted proteins for discovery of different proteins before and after IVR treatment in the same patient. (frontiersin.org)
Based on the protein-protein interaction (PPI) network analysis, core targets and core subsets were screened. (hindawi.com)
Then, the relationship between the expression level of the core genes and the prognosis of gastric cancer patients was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA) database. (hindawi.com)
Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. (asm.org)
Based on the tumor purity and lung carcinoma gene matrix, we performed weighted gene coexpression network analysis (WGCNA), and the tumor purity-related module was identified. (hindawi.com)
In this study, we constructed a tumor purity coexpression network based on weighted gene coexpression network analysis (WGCNA) [ 8 ]. (hindawi.com)
Weighted gene correlation network analysis (WGCNA) can identify groups of biologically related proteins using only protein intensity values by constructing protein correlation networks. (stanford.edu)
We demonstrate MetaNetwork's utility by employing it to identify groups of proteins associated with prostate cancer from a proteomic analysis of tumor and adjacent normal tissue samples. (stanford.edu)
The minimal set of genes obtained is a function of which and how many genomes are chosen for the analysis. (cns.fr)
BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. (sri.com)
The analysis provided a list of gene targets for engineering ethanol tolerance in cyanobacterium Synechocystis . (biomedcentral.com)

An increasing number of GO-mapped sequence databases make it possible to replace traditional database searches with GO-related searches. (biomedcentral.com)
Search dbEST , dbSTS , dbGSS general genome sequence databases. (fiocruz.br)

11 proteins were up-regulated and 17 proteins were down-regulated, while consistent presence/absence expression profile group contains one elevated protein and nine reduced proteins, among which seven proteins were identified as potential biomarkers for IVR treatment through PRM assays. (frontiersin.org)

In response to low temperature, many biochemical and physiological processes change in plants through regulation of cold responsive (COR) gene expression as well as through posttranslational protein modifications. (biomedcentral.com)
The advent of genome sequencing revealed in humans and other species thousands of genes encoding proteins that had not been identified by previous biochemical or genetic studies. (biorxiv.org)

CRISPR/Cas9 gene disruption validated a component of Notch signalling and two genes contributing to male fertility. (biorxiv.org)

GO provides consistent descriptions of gene products in a species-independent manner. (biomedcentral.com)
Colonization of the gut starts just after birth when pioneering species interact, through surface receptors, with gut cells to promote the expression of a specific set of host genes and favour the colonization of commensal microorganisms [6]. (deepdyve.com)
Our results suggest that cold temperature significantly affects genes related to protein translation and cellular metabolism in this chilling sensitive species. (biomedcentral.com)
Now in its 10th year, the Gramene database ( http://www.gramene.org ) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. (oregonstate.edu)

Five coexpressed genes (CD4, CD53, EVI2B, PLEK, and SASH3) were identified as tumor purity coexpressed genes that negatively correlated with tumor purity. (hindawi.com)
OncoKB currently contains 4472 alterations for 595 genes of 38 tumor types. (lu.se)

An integrated genetic and cytogenetic map of the cucumber genome. (gao-lab.org)

In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including bla VIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. (who.int)

Using the GSE19826 and GSE54129 datasets, a total of 550 DEGs were identified, including 248 upregulated and 302 downregulated genes. (hindawi.com)

Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)

P22 has strong 16S rRNA gene sequence similarity to Paenibacillus humicus (99.5%) ( 7 ). (asm.org)

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)

Additionally, 193 cytochrome P450 (CYP450), 280 methyltransferase and 144 isomerase genes were identified, that are potential candidates for enzymes involved in RIN and IRN synthesis. (biomedcentral.com)

Bacteria database (VFDB) and Pathogen-Host Interactions database (PHI). (cdc.gov)
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)

Anatomy8

Organisms19

Diseases3

Chemicals and Drugs34

Analytical, Diagnostic and Therapeutic Techniques and Equipment36

Phenomena and Processes119

Disciplines and Occupations8

Technology, Industry, Agriculture4

Information Science50

Health Care11

Ontology12

Sequences15

Whole genome4

Kyoto Encyclo2

NCBI2

KEGG1

Human Genome5

Pathways6

Bioinformatics12

RefSeq6

Organism6

Genomic8

Variants3

Metabolic3

Prediction1

Differentially expressed genes4

Complete Genome Sequence2

Pathway2

Candidate genes2

Identifying genes encodin1

Structural1

Core-genome1

Contigs2

Encodes1

Isolates6

Metagenomics1

Classification1

Computational4

20,0001

Pipeline2

Analyses3

Microbial4

Evolutionary1

Kinase4

Biological6

Microarray2

Bacterial5

Biosynthesis2

Phylogenetic2

Predict4

Mutations6

Orthologs1

Analysis12

Sequence databases2

Biomarkers1

Biochemical2

Cas91

Species4

Tumor2

Genetic1

Resistance genes1

DEGs1

Datasets1

RRNA gene sequence1

Synteny3

Enzymes involved1

Interactions2