PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Functional genes”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8Linked to original sources
PubMed1994

Organization and chromosomal assignment of two human PAG gene loci: PAGA encoding a functional gene and PAGB a processed pseudogene.

A cDNA, designated PAG, was recently isolated by differential cloning between an untransformed and a ras-transformed human mammary cell line. Higher levels of expression were found to be associated with cell proliferation. The absence in the pag protein of known consensus sequence, as well as its close relationship with a gene product involved in the differentiation of a mouse erythroleukemia cell line, has suggested that the PAG gene belongs to a family of genes associated with cell proliferation and differentiation. To further characterize this gene, a physical map has been established from a human genomic cosmid library. The PAG gene spans 13 kb of DNA and contains six exons. The promoter region is GC-rich and contains a TFIID motif located 25 nucleotides upstream of the potential site for initiation of transcription and potential recognition sites for a variety of trans-acting factors. Using fluorescence in situ hybridization, the PAG gene was mapped to human chromosome band 1p34.1. A pseudogene was also isolated, sequenced, and mapped to human chromosome band 9p22.

Base Sequence↗
PubMed2001

The green fluorescent protein gene functions as a reporter of gene expression in Phanerochaete chrysosporium.

The enhanced green fluorescent protein (GFP) gene (egfp) was used as a reporter of gene expression driven by the glyceraldehyde-p-dehydrogenase (gpd) gene promoter and the manganese peroxidase isozyme 1 (mnp1) gene promoter in Phanerochaete chrysosporium. Four different constructs were prepared. pUGGM3' and pUGiGM3' contain the P. chrysosporium gpd promoter fused upstream of the egfp coding region, and pUMGM3' and pUMiGM3' contain the P. chrysosporium mnp1 promoter fused upstream of the egfp gene. In all constructs, the egfp gene was followed by the mnp1 gene 3' untranslated region. In pUGGM3' and pUMGM3', the promoters were fused directly with egfp, whereas in pUGiGM3' and pUMiGM3', following the promoters, the first exon (6 bp), the first intron (55 bp), and part of the second exon (9 bp) of the gpd gene were inserted at the 5' end of the egfp gene. All constructs were ligated into a plasmid containing the ura1 gene of Schizophyllum commune as a selectable marker and were used to transform a Ural1 auxotrophic strain of P. chrysosporium to prototrophy. Crude cell extracts were examined for GFP fluorescence, and where appropriate, the extracellular fluid was examined for MnP activity. The transformants containing a construct with an intron 5' of the egfp gene (pUGiGM3' and pUMiGM3') exhibited maximal fluorescence under the appropriate conditions. The transformants containing constructs with no introns exhibited minimal or no fluorescence. Northern (RNA) blots indicated that the insertion of a 5' intron resulted in more egfp RNA than was found in transformants carrying an intronless egfp. These results suggest that the presence of a 5' intron affects the expression of the egfp gene in P. chrysosporium. The expression of GFP in the transformants carrying pUMiGM3' paralled the expression of endogenous mnp with respect to nitrogen and Mn levels, suggesting that this construct will be useful in studying cis-acting elements in the mnp1 gene promoter.

Base Sequence↗
PubMed1993

Genomic structure of growth hormone genes in chinook salmon (Oncorhynchus tshawytscha): presence of two functional genes, GH-I and GH-II, and a male-specific pseudogene, GH-psi.

Two chinook salmon (Oncorhynchus tshawytscha) growth hormone genes (a functional GH-I gene and a pseudogene, GH-psi) were isolated and characterized. The GH-I gene sequence consists of 1.9 kb of 5'-flanking sequence, 4.1 kb of transcribed region, and 64 bp of 3'-flanking sequence, and contains 6 exons and 5 introns. The pseudogene, GH-psi, spanning 4.1 kb, has a similar structure as the GH-I gene. However, it has one wrong splicing sequence at the intron 1/exon 2 junction, one premature termination codon in exon 5, and a deletion in the last half of exon 5 and the first part of intron 5. In addition to GH-I gene and GH-psi, a third GH gene, GH-II, was identified by the polymerase chain reaction (PCR) and subsequently shown to be the second functional GH-II gene. To study the linkage arrangement of these three GH genes, 50 unrelated chinook salmon (25 males and 25 females) and one chinook salmon family were analyzed by PCR. The results showed that GH-psi exists only in males and that it segregates from father to sons. These results suggest that GH-psi is sex specific and probably resides on the Y chromosome. Together these results indicate that there are three GH genes in the genome of male chinook salmon, and only two GH genes in the females. The extra GH gene in the male is, however, a pseudogene.

Amino Acid Sequence↗
PubMed1999

Application of antisense oligonucleotides for gene functionalization and target validation.

The Human Genome Project (complete sequencing of the human genome) will be complete soon and the information made available to the biomedical community. Although the project is not yet complete, it has dramatically changed the practice of biomedical sciences. With enormous amounts of information available from sequencing efforts, increasing demands are being put on researchers to quickly determine the biochemical function of novel molecular targets and to validate them as appropriate for drug discovery endeavors. Antisense oligonucleotides are an ideal technology for gene functionalization and target validation. They are an efficient methodology for gene functionalization and target validation and are a proven technology. Antisense technology can answer questions with a high degree of precision and it is a versatile technology. In this review the use of antisense oligonucleotides as a research tool for gene functionalization and target validation is discussed.

Animals↗
PubMed1982

Recombination between two IS/s flanking the r-determinant of R100-1: involvement of dor and recA gene functions in Salmonella typhimurium.

Drug resistance genes of the r-determinant component of a composite R plasmid R100-1 were frequently lost in Salmonella typhimurium. Various deletion mutants were analyzed by restriction endonuclease cleavage, Southern blotting, and hybridization techniques. The loss of the r-determinant was found to be the result of a reciprocal recombination between the two IS/s flanking the r-determinant. This recombination depended upon both dor and recA gene functions.

Base Sequence↗
PubMed2006

VIRGO: computational prediction of gene functions.

Dramatic advances in sequencing technology and sophisticated experimental assays that interrogate the cell, combined with the public availability of the resulting data, herald the era of systems biology. However, the biological functions of more than 40% of the genes in sequenced genomes are unknown, posing a fundamental barrier to progress in systems biology. The large scale and diversity of available data requires the development of techniques that can automatically utilize these datasets to make quantified and robust predictions of gene function that can be experimentally verified. We present a service called the VIRtual Gene Ontology (VIRGO) that (i) constructs a functional linkage network (FLN) from gene expression and molecular interaction data, (ii) labels genes in the FLN with their functional annotations in the Gene Ontology and (iii) systematically propagates these labels across the FLN in order to precisely predict the functions of unlabelled genes. VIRGO assigns confidence estimates to predicted functions so that a biologist can prioritize predictions for further experimental study. For each prediction, VIRGO also provides an informative 'propagation diagram' that traces the flow of information in the FLN that led to the prediction. VIRGO is available at http://whipple.cs.vt.edu:8080/virgo.

Algorithms↗
PubMed2001

Antisense display: a new method for functional gene screen and its application to angiogenesis-related gene isolation.

We have developed an antisense-oriented method for functional gene screening, which we termed "antisense display." After evaluation in a cell-free system, we applied this method to a cellular system for isolating angiogenesis-related genes and came across a gene previously not described in humans. A screen of 10 mer antisense repertoire led to the identification of a unique 'angiostatic' antisense, and the gene corresponding to it was found to be preferentially expressed in vascular endothelial cells, coding for a putative type-2 membrane protein containing Rab-GAP/TBC and EF-hand-like domains. We named it vascular Rab-GAP/TBC domain-containing protein (VRP). The results obtained thus indicate that the antisense display method is useful for the isolation of functional genes responsible for phenotypes concerned.

Genetic Testing↗
PubMed2003

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).

Genomic sequencing is no longer a novelty, but gene function annotation remains a key challenge in modern biology. A variety of functional genomics experimental techniques are available, from classic methods such as affinity precipitation to advanced high-throughput techniques such as gene expression microarrays. In the future, more disparate methods will be developed, further increasing the need for integrated computational analysis of data generated by these studies. We address this problem with MAGIC (Multisource Association of Genes by Integration of Clusters), a general framework that uses formal Bayesian reasoning to integrate heterogeneous types of high-throughput biological data (such as large-scale two-hybrid screens and multiple microarray analyses) for accurate gene function prediction. The system formally incorporates expert knowledge about relative accuracies of data sources to combine them within a normative framework. MAGIC provides a belief level with its output that allows the user to vary the stringency of predictions. We applied MAGIC to Saccharomyces cerevisiae genetic and physical interactions, microarray, and transcription factor binding sites data and assessed the biological relevance of gene groupings using Gene Ontology annotations produced by the Saccharomyces Genome Database. We found that by creating functional groupings based on heterogeneous data types, MAGIC improved accuracy of the groupings compared with microarray analysis alone. We describe several of the biological gene groupings identified.

Algorithms↗
PubMed2004

Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae.

Characterizing gene function is one of the major challenging tasks in the post-genomic era. To address this challenge, we have developed GeneFAS (Gene Function Annotation System), a new integrated probabilistic method for cellular function prediction by combining information from protein-protein interactions, protein complexes, microarray gene expression profiles, and annotations of known proteins through an integrative statistical model. Our approach is based on a novel assessment for the relationship between (1) the interaction/correlation of two proteins' high-throughput data and (2) their functional relationship in terms of their Gene Ontology (GO) hierarchy. We have developed a Web server for the predictions. We have applied our method to yeast Saccharomyces cerevisiae and predicted functions for 1548 out of 2472 unannotated proteins.

Automation↗
PubMed2005

Learning yeast gene functions from heterogeneous sources of data using hybrid weighted Bayesian networks.

We developed a machine learning system for determining gene functions from heterogeneous sources of data sets using a Weighted Naive Bayesian Network (WNB). The knowledge of gene functions is crucial for understanding many fundamental biological mechanisms such as regulatory pathways, cell cycles and diseases. Our major goal is to accurately infer functions of putative genes or ORFs (Open Reading Frames) from existing databases using computational methods. However, this task is intrinsically difficult since the underlying biological processes represent complex interactions of multiple entities. Therefore many functional links would be missing when only one or two source of data is used in the prediction. Our hypothesis is that integrating evidence from multiple and complementary sources could significantly improve the prediction accuracy. In this paper, our experimental results not only suggest that the above hypothesis is valid, but also provide guidelines for using the WNB system for data collection, training and predictions. The combined training data sets contain information from gene annotations, gene expressions, clustering outputs, keyword annotations and sequence homology from public databases. The current system is trained and tested on the genes of budding yeast Saccharomyces cerevisiae. Our WNB model can also be used to analyze the contribution of each source of information toward the prediction performance through the weight training process. The contribution analysis could potentially lead to significant scientific discovery by facilitating the interpretation and understanding of the complex relationships between biological entities.

Artificial Intelligence↗
PubMed2001

ENU mutagenesis: analyzing gene function in mice.

With the completion of the human genome, sequence analysis of gene function will move into the center of future genome research. One of the key strategies for studying gene function involves the genetic dissection of biological processes in animal models. Mouse mutants are of particular importance for the analysis of disease pathogenesis and transgenic techniques, and gene targeting have become routine tools. Recently, phenotype-driven strategies using chemical mutagenesis have been the target of increasing interest. In this review, the current state of ENU mutagenesis and its application as a systematic tool of genome analysis are examined.

Animals↗
PubMed2006

Gene function correlates with potential for G4 DNA formation in the human genome.

G-rich genomic regions can form G4 DNA upon transcription or replication. We have quantified the potential for G4 DNA formation (G4P) of the 16 654 genes in the human RefSeq database, and then correlated gene function with G4P. We have found that very low and very high G4P correlates with specific functional classes of genes. Notably, tumor suppressor genes have very low G4P and proto-oncogenes have very high G4P. G4P of these genes is evenly distributed between exons and introns, and it does not reflect enrichment for CpG islands or local chromosomal environment. These results show that genomic structure undergoes selection based on gene function. Selection based on G4P could promote genomic stability (or instability) of specific classes of genes; or reflect mechanisms for global regulation of gene expression.

CpG Islands↗
PubMed2005

Studying the consequences of immediate loss of gene function in the intestine: APC.

The use of mouse models to study neoplasia is proving particularly powerful in dissecting the mechanisms underlying disease initiation and progression. However, the majority of these models have been somewhat limited in studying the very early effects of loss of gene function, as tumour initiation relies upon either constitutive loss of gene function or spontaneous somatic loss of function. We have therefore adopted a strategy of using an inducible Cre-lox-based system to analyse the effects of loss of gene function, the use of which is reviewed here for the intestinal tumour suppressor APC (adenomatous polyposis coli). Using this approach, we have conditionally and synchronously inactivated APC in virtually all the epithelial cells of the adult murine small intestine. After 5 days following induction of Cre-mediated recombination, mice show grossly altered crypt/villus architecture. Deficiency in APC perturbs migration, alters the normal programme of differentiation and results in increased proliferation and apoptosis. Microarray analysis reveals the transcriptome to be significantly altered; reflecting both gross phenotypic changes and changes in transcriptional activation. These findings demonstrate that APC is indeed the critical determinant of cell fate in the intestinal epithelium, explaining its role as the cellular 'gatekeeper' in preventing neoplasia.

Adenomatous Polyposis Coli↗
PubMed2006

Teaching molecular genetics: chapter 2-Transgenesis and gene targeting: mouse models to study gene function and expression.

Many human diseases result from the (partial) loss of gene function. Once a disease-causing gene has been identified, a wide variety of techniques can be used to study its function, structure and expression. Many clues can be obtained from the comparison of RNA or proteins in tissues, cell extracts or cell lines at different physiological or developmental stages. Since the mouse genome is very similar to the human genome, expression data from mice are extremely valuable. Recently developed techniques to add genes to the mouse genome or to modify or inactivate genes form powerful tools to analyze gene function and expression. For a variety of human diseases these genetically modified mice are very informative model systems.

Animals↗
PubMed2003

An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof.

The Arabidopsis genome sequencing in 2000 gave to science the first blueprint of a vascular plant. Its successful completion also prompted the US National Science Foundation to launch the Arabidopsis 2010 initiative, the goal of which is to identify the function of each gene by 2010. In this study, an exhaustive analysis of The Institute for Genomic Research (TIGR) and The Arabidopsis Information Resource (TAIR) databases, together with all currently compiled EST sequence data, was carried out in order to determine to what extent the various metabolic networks from phenylalanine ammonia lyase (PAL) to the monolignols were organized and/or could be predicted. In these databases, there are some 65 genes which have been annotated as encoding putative enzymatic steps in monolignol biosynthesis, although many of them have only very low homology to monolignol pathway genes of known function in other plant systems. Our detailed analysis revealed that presently only 13 genes (two PALs, a cinnamate-4-hydroxylase, a p-coumarate-3-hydroxylase, a ferulate-5-hydroxylase, three 4-coumarate-CoA ligases, a cinnamic acid O-methyl transferase, two cinnamoyl-CoA reductases) and two cinnamyl alcohol dehydrogenases can be classified as having a bona fide (definitive) function; the remaining 52 genes currently have undetermined physiological roles. The EST database entries for this particular set of genes also provided little new insight into how the monolignol pathway was organized in the different tissues and organs, this being perhaps a consequence of both limitations in how tissue samples were collected and in the incomplete nature of the EST collections. This analysis thus underscores the fact that even with genomic sequencing, presumed to provide the entire suite of putative genes in the monolignol-forming pathway, a very large effort needs to be conducted to establish actual catalytic roles (including enzyme versatility), as well as the physiological function(s) for each member of the (multi)gene families present and the metabolic networks that are operative. Additionally, one key to identifying physiological functions for many of these (and other) unknown genes, and their corresponding metabolic networks, awaits the development of technologies to comprehensively study molecular processes at the single cell level in particular tissues and organs, in order to establish the actual metabolic context.

Arabidopsis↗
PubMed1998

Escherichia coli dnaA gene function and bacteriophage lambda replication.

Allele specificity of the Escherichia coli dnaA gene function in the replication of plasmids derived from bacteriophage lambda has been demonstrated previously. Here, using a series of dnaA temperature-sensitive mutants, we investigated dnaA allele specificity of the replication of phages lambda P+ and lambda Pts 1 pi A66. We found that phage lambda P+ produces its progeny efficiently at 43 degrees C irrespective of the dnaA allele, whereas lambda Pts 1 pi A66, which is unable to develop lytically in the dnaA+ host at this temperature, can replicate with different efficiency in certain dnaA mutants. Since the main role of DnaA in lambda development seems to be stimulation of transcription from the pR promoter, we measured the activity of this promoter (using a pR-lacZ fusion) and the abundance of pR-derived transcripts (by Northern blotting analysis) in dnaA+ host and dnaA(ts) mutants at 30 and 43 degrees C. We found significant differences in the activity of pR in various dnaA(ts) mutants at 30 degrees C, which indicate different levels of stimulation of this promoter by products of particular dnaA alleles at permissive temperature. Differential levels of DnaA-mediated stimulation of pR in various dnaA(ts) mutants were also found at 43 degrees C. Stimulation of the pR promoter by DnaA is necessary for both efficient production of the lambda replication proteins, O and P, and effective transcriptional activation of ori lambda. The differences in the efficiency of pR activation observed in dnaA mutants at 30 and 43 degrees C can explain the mechanisms of allele specificity of dnaA gene function in the replication of bacteriophage lambda and plasmids derived from this phage.

Alleles↗
PubMed2001

Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.

Gene order in prokaryotes is conserved to a much lesser extent than protein sequences. Only several operons, primarily those that code for physically interacting proteins, are conserved in all or most of the bacterial and archaeal genomes. Nevertheless, even the limited conservation of operon organization that is observed can provide valuable evolutionary and functional clues through multiple genome comparisons. A program for constructing gapped local alignments of conserved gene strings in two genomes was developed. The statistical significance of the local alignments was assessed using Monte Carlo simulations. Sets of local alignments were generated for all pairs of completely sequenced bacterial and archaeal genomes, and for each genome a template-anchored multiple alignment was constructed. In most pairwise genome comparisons, <10% of the genes in each genome belonged to conserved gene strings. When closely related pairs of species (i.e., two mycoplasmas) are excluded, the total coverage of genomes by conserved gene strings ranged from <5% for the cyanobacterium Synechocystis sp to 24% for the minimal genome of Mycoplasma genitalium, and 23% in Thermotoga maritima. The coverage of the archaeal genomes was only slightly lower than that of bacterial genomes. The majority of the conserved gene strings are known operons, with the ribosomal superoperon being the top-scoring string in most genome comparisons. However, in some of the bacterial-archaeal pairs, the superoperon is rearranged to the extent that other operons, primarily those subject to horizontal transfer, show the greatest level of conservation, such as the archaeal-type H+-ATPase operon or ABC-type transport cassettes. The level of gene order conservation among prokaryotic genomes was compared to the cooccurrence of genomes in clusters of orthologous genes (COGs) and to the conservation of protein sequences themselves. Only limited correlation was observed between these evolutionary variables. Gene order conservation shows a much lower variance than the cooccurrence of genomes in COGs, which indicates that intragenome homogenization via recombination occurs in evolution much faster than intergenome homogenization via horizontal gene transfer and lineage-specific gene loss. The potential of using template-anchored multiple-genome alignments for predicting functions of uncharacterized genes was quantitatively assessed. Functions were predicted or significantly clarified for approximately 90 COGs (approximately 4% of the total of 2414 analyzed COGs). The most significant predictions were obtained for the poorly characterized archaeal genomes; these include a previously uncharacterized restriction-modification system, a nuclease-helicase combination implicated in DNA repair, and the probable archaeal counterpart of the eukaryotic exosome. Multiple genome alignments are a resource for studies on operon rearrangement and disruption, which is central to our understanding of the evolution of prokaryotic genomes. Because of the rapid evolution of the gene order, the potential of genome alignment for prediction of gene functions is limited, but nevertheless, such predictions information significantly complements the results obtained through protein sequence and structure analysis.

Computational Biology↗