Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

NEIBank is a project to develop and organize genomics and bioinformatics resources for the eye. As part of this effort, tools have been developed for bioinformatics analysis and web based display of data from expressed sequence tag (EST) analyses. EST sequences are identified and formed into groups or clusters representing related transcripts from the same gene. This is carried out by a rules-based procedure called GRIST (GRouping and Identification of Sequence Tags) that uses sequence match parameters derived from BLAST programs. Linked procedures are used to eliminate non-mRNA contaminants. All data are assembled in a relational database and assembled for display as web pages with annotations and links to other informatics resources. Genome projects generate huge amounts of data that need to be classified and organized to become easily accessible to the research community. GRIST provides a useful tool for assembling and displaying the results of EST analyses. The NEIBank web site contains a growing set of pages cataloging the known transcriptional repertoire of eye tissues, derived from new NEIBank cDNA libraries and from eye-related data deposited in the dbEST section of GenBank.
Mol Vis 2002 Jun 15
PMID:Grouping and identification of sequence tags (GRIST): bioinformatics tools for the NEIBank database. 1210 14

VCP (Valosin-Containing Protein), a member of the AAA (ATPases Associated to a variety of cellular Activities) family of proteins, possesses a duplicated highly conserved ATPase domain. An expressed sequence tag (EST), representing a clone from the Eimeria tenella merozoite cDNA library, was found to have high similarity to VCP genes from other organisms. A complete sequence derived from the corresponding clone (designated eth060) shows amino acid identity of 42-62% with other members of the VCP subfamily. Sequence analysis identified a putative ATPase domain in the eth060 sequence. This domain was PCR-amplified using gene-specific primers and cloned into a pBAD/Thio-TOPO expression vector. Expression in Escherichia coli demonstrated that the putative ATPase domain, which consists of 414 amino acid residues, produced a fusion protein of approximately 60 kDa in size.
J Biochem Mol Biol Biophys 2002 Apr
PMID:Molecular characterization and expression of a putative ATPase domain from Eimeria tenella. 1218 68

The gene expression profiles of 146 novel ESTs were characterized in newborn and adult rat brains via radioactive in situ hybridization. Using Euclidean metrics and hierarchical clustering tools the brain expression profiles obtained clustered into seven synexpression groups. The groups were: I, non-detectable expression (68 ESTs); II, low expression in hippocampus (40 ESTs); III, low expression in adult, high expression in newborn (two ESTs); IV, medium expression throughout brain (31 ESTs); V, high expression throughout brain (three ESTs); VI, selective high expression in hippocampus, caudate and putamen (one EST); VII, selective high expression in hippocampus (one EST). Five ESTs were expressed in the striatum and three responded transcriptionally to neuroleptic and neuroprotective drug treatments, suggesting that this approach could be used to detect novel drug targets. These results provide a useful starting point to explore the functional genomics of genes without known functions forthcoming from various genome projects.
Brain Res Mol Brain Res 2002 Aug 15
PMID:Synexpression analysis of ESTs in the rat brain reveals distinct patterns and potential drug targets. 1222 72

We have investigated three different microarray datasets of approximately 6 K gene expressions across the National Cancer Institute's panel of 60 tumor cell lines. Initial assessments of reproducibility for gene expressions within each dataset, as derived from sequence analysis of full-length sequences as well as expressed sequence tags (EST), found statistically significant results for no more than 36% of those cases where at least one replicate of a gene appears on the array. Filtering the data based only on pairwise comparisons among these three datasets creates a list of approximately 400 significant concordant expression patterns. The expression profiles of these smaller sets of genes were used to locate similar expression profiles of synthetic agents screened against these same 60 tumor cell lines. A correspondence was found between mRNA expression patterns and 50% growth inhibition response patterns of screened agents for 11 cases that were subsequently verifiable from ligand-target crystallographic data. Notable amongst these cases are genes encoding a variety of kinases, which were also found to be targets of small drug-like molecules within the database of protein structures. These 11 cases lend support to the premise that similarities between expression patterns and chemical responses for the National Cancer Institute's tumor panel can be related to known cases of molecular structure and putative cellular function. The details of the 11 verifiable cases and the concordant gene subsets are provided. Discussions about the prospects of using this approach as a data mining tool are included.
Mol Cancer Ther 2002 Mar
PMID:Establishing connections between microarray expression data and chemotherapeutic cancer pharmacology. 1248 47

We report on the cloning and characterization of a novel gene EC97 which is associated with human esophageal squamous cell carcinoma (ESCC). A fragment of expressed sequence tag (EST) (aa700351) was overexpressed in ESCC tissues compared with the normal tissues in cDNA microarray data. Based on the sequence of aa700351, the full-length cDNA was acquired by polymerase chain reaction (PCR) amplification and named EC97. EC97 was 3353 bp long and its encoding protein contained 813 amino acid residues. Northern blot and reverse transcription polymerase chain reaction (RT-PCR) analysis revealed that EC97 had a transcript of 3.4 kb in most human normal tissues we checked and its expression level was increased in 60% (12/20) of tested ESCC tissues versus the normal counterparts. EC97 was mapped to human chromosome 16p12-16p13.1 using radiation hybridization (RH) and predicted to include 25 exons and disseminated over 100 kb of genomic DNA.
Int J Mol Med 2003 Feb
PMID:Cloning and characterization of a novel gene EC97 associated with human esophageal squamous cell carcinoma. 1252 86

Gene expression analysis comparing nonpregnant with pregnant bovine uteri, including placenta, was performed with a custom cDNA microarray containing 1,933 independent genes. These genes were classified into six categories according to biological function, as follows: cell and tissue structural dynamics (108 genes), intercellular communication (221), intracellular metabolism (265), cell cycle and apoptosis (26), regulation of gene expression (113), expressed sequence tag (EST) and function unknown (617), and uncomplemented genes (583 clones). This array possessed bovine placental/endometrial specificity, as it included many pregnancy-specific molecules, such as pregnancy-associated glycoprotein-1 (PAGs), placental lactogen (PLs), and prolactin-related protein-1 (PRPs). A total of 77 genes were induced and 12 repressed in the placenta/endometrium. Our results point to a fundamental role for bovine placental-specific genes such as PAGs, PLs, and PRPs, in implantation and placentogenesis, and document that cDNA microarray analysis from bovine placenta/endometrium is possible and is a specific tool for monitoring genome-wide gene expression during the establishment and maintenance of pregnancy.
Mol Reprod Dev 2003 May
PMID:Characterization of gene expression profiles in early bovine pregnancy using a custom cDNA microarray. 1265 28

Ubiquitin is a small, highly conserved protein found in all eukaryotic cells. Through its covalent attachment to other proteins, ubiquitin regulates numerous important cellular processes including apoptosis, transcription, and the progression of the cell cycle. Ubiquitin expression is unusual: it is encoded and expressed as multimeric head-to-tail repeats (polyubiquitins) that are post-translationally cleaved into monomers, or fused with ribosomal proteins L40 and S27a. The ubiquitin moiety is removed from these fusion proteins, but is thought to act as a chaperone in ribosome biogenesis prior to cleavage. Here we show that the chlorarachniophyte algae express several novel ubiquitin fusion proteins. An expressed sequence tag (EST) survey revealed ubiquitin fusions with an unidentified open reading frame (ORF), ribosomal protein P1 and, most interestingly, actin. Actin is an essential component of the eukaryotic cytoskeleton and is involved in a variety of cellular processes. In other eukaryotes, actin genes only exist as stand-alone ORFs, but in all chlorarachniophytes examined, actin is always encoded as a ubiquitin fusion protein. The variety of ubiquitin fusion proteins in these organisms raises interesting questions about the evolutionary origins of ubiquitin fusions, as well as their possible biochemical functions in other processes, such as cytoskeletal regulation.
J Mol Biol 2003 May 09
PMID:Novel ubiquitin fusion proteins: ribosomal protein P1 and actin. 1272 53

Significant changes in root morphology and physiology during arbuscular mycorrhiza (AM) development are likely to be controlled by specific gene expression pattern in the host plant. Until now, little was known about transcriptional changes which occur AM-exclusively; that is, they do not occur during other root-microbe associations, nor are they induced by improved phosphate nutrition. In order to identify such AM-exclusive gene inductions of Medicago truncatula, we used a pool of different RNA samples as subtractor population in a suppressive subtractive hybridization (SSH) experiment. This approach resulted in the identification of a number of new AM-regulated genes. None of these genes were expressed in nonmycorrhiza roots or leaves. Electronic data obtained by comparison of the cDNA sequences to expressed sequence tag (EST) sequences from a wide range of cDNA libraries in the M. truncatula EST database (Gene Index, MtGI) support the mycorrhiza specificity of the corresponding genes, because sequences in the MtGI that were found to match the identified SSH-cDNA sequences originated exclusively from AM cDNA libraries. The promoter of one of those genes, MtGst1, showing similarities to plant glutathione-S-transferase (GST) encoding genes, was cloned and used in reporter gene studies. In contrast to studies with the potato GST gene PRP, MtGst 1 promoter activity was detected in all zones of the root cortex colonized by Glomus intraradices, but nowhere else.
Mol Plant Microbe Interact 2003 Apr
PMID:Transcriptional changes in response to arbuscular mycorrhiza development in the model plant Medicago truncatula. 1274 59

Genomic DNA was extracted from heartwood blocks of six Cryptomeria japonica individuals that had been buried (in an area now covered by rice fields) for about 3600 years. Attempts were made to determine the sequences of five nuclear genes following polymerase chain reaction amplification, using previously obtained C. japonica expressed sequence tag (EST) information. We detected 15 nucleotide substitutions and four insertion/deletions (indels) in a partial GapC gene sequence among 13 individuals of the buried and an extant population, which allowed us to estimate the extent of DNA variation within the buried populations, and the level of genetic differentiation between the buried population and the extant population growing in a neighbouring area. For the entire haplotypes of the GapC region, pi and theta nucleotide diversity estimates were 0.0063 and 0.0010, respectively, when both populations were included, while corresponding figures for the buried population alone were 0.0009 and 0.0017. Estimates of DNA divergence statistics (dXY = 0.0062, dA = 0.0005, FST = 0.0832 and KST = 0.0935) suggest that differentiation between the two populations was not great. However, permutation tests gave FST and KST values rejecting the null hypothesis (that populations were not differentiated) at the 5% and 1% probability levels, respectively. The significant genetic differentiation between the two populations was mainly caused by differences in haplotype diversity. The significant level of haplotype diversity in the extant population compared to the buried population might be the result of gene flow from neighbouring artificial forests. Alternatively, it is possible that we failed to detect all the DNA variation in the buried population because of clonal growth in the buried population.
Mol Ecol 2003 Apr
PMID:Nuclear gene sequences and DNA variation of Cryptomeria japonica samples from the postglacial period. 1275 7

The vacuolar-type ATPase (V-ATPase) and the vacuolar H(+)-pyrophosphatase are electrogenic proton pumps at plant endomembranes that create the proton motive force required for secondary activated transport and metabolite accumulation during development and adaptation to a variety of adverse growth conditions. Twelve distinct vacuolar H(+)-ATPase (VHA) subunits are suggested to constitute the functional V-ATPase complex. Starting from the available expressed sequence tag (EST) sequences and by homology screening, the complete set of 12 VHA subunits was cloned as cDNAs from the halophyte Mesembryanthemum crystallinum, vha-A-H, -a,-c, -d and -e. Transcript levels of all 12 VHA subunits as well as of tonoplast pyrophosphatase and P-ATPase were analysed in root and leaf tissue under conditions of osmotic (700 mM mannitol), heat and cold stress, and salinity. Distinct coordinated changes of stress-induced expression were observed for most subunits in roots and leaves, with mostly paralleled changes in transcript levels of all subunits. In some cases, contrasting responses were seen for vha-B and -c transcript amounts.
Mol Membr Biol
PMID:cDNA cloning of 12 subunits of the V-type ATPase from Mesembryanthemum crystallinum and their expression under stress. 1285 Oct 73


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