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At least 541 records · Page 30Linked to original sources
PubMed1991

Histochemical localization of gene expression in Onchocerca volvulus: in situ DNA histohybridization and immunocytochemistry.

We report here the development of in situ hybridization and immunohistochemistry protocols which permit the histological identification of gene expression of a cloned antigen of Onchocerca volvulus, OI5, in the parasite. Skin nodules containing female adult worms were fixed in a modified Carnoy's fixative and embedded in paraffin. Histological staining of tissue sections revealed uniformly excellent morphology and RNA preservation. To localize mRNA by in situ hybridization, tissue sections were incubated with biotin-labeled pOI5, the plasmid containing the genomic sequence of the antigen, and hybridization signals were histochemically visualized using a streptavidin-enzyme conjugate and chromogenic substrates. The protein antigen was localized immunohistochemically by incubating the sections with specific antibodies prepared against a recombinant fusion protein containing the OI5 sequence (OI3), and visualized via a secondary antibody-biotin-enzyme conjugate procedure. The results reported here showed distinct localization of the OI5 mRNA and OI3 antigen in specific cellular and tissue regions of the adult parasite, and in microfilariae located within the uteri and in the surrounding host tissue. The specificity and high sensitivity of these histological detection methods should be generally applicable for the characterization of gene expression in the filarial parasite, particularly the insect-borne, infective filarial larvae, which are severely limited in quantity.

Animals↗
PubMed2005

Leber's hereditary optic neuropathy is associated with the mitochondrial ND4 G11696A mutation in five Chinese families.

We report here the clinical, genetic, and molecular characterization of five Chinese families with Leber's hereditary optic neuropathy (LHON). Clinical and genetic evaluations revealed the variable severity and age-of-onset in visual impairment in these families. Strikingly, there were extremely low penetrances of visual impairment in these Chinese families. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the distinct sets of mtDNA polymorphism, in addition to the identical ND4 G11696A mutation associated with LHON. Indeed, this mutation is present in homoplasmy only in the maternal lineage of those pedigrees but not other members of these families. In fact, the occurrence of the G11696A mutation in these several genetically unrelated subjects affected by visual impairment strongly indicates that this mutation is involved in the pathogenesis of visual impairment. Furthermore, the N405D in the ND5 and G5820A in the tRNA(Cys), showing high evolutional conservation, may contribute to the phenotypic expression of G11696A mutation in the WZ10 pedigree. However, there was the absence of functionally significant mtDNA mutations in other four Chinese pedigrees carrying the G11696A mutation. Therefore, nuclear modifier gene(s) or environmental factor(s) may play a role in the phenotypic expression of the LHON-associated G11696A mutation in these Chinese pedigrees.

Adolescent↗
PubMed2001

Single-tube two-round polymerase chain reaction using the LightCycler instrument.

BACKGROUND: For many diagnostic applications, the specificity and sensitivity of polymerase chain reaction (PCR) is markedly enhanced by applying two rounds of PCR with nested or semi-nested pairs of primers. In two-round PCR protocols on the LightCycler instrument, amplification products must be collected from the capillaries by centrifugation, a procedure thought to be particularly prone to product carry-over. OBJECTIVE: Development of a technique to perform two-round PCR with the LightCycler instrument in a single closed capillary. STUDY DESIGN: Silicone oil was used to separate the second-round primers from first-round PCR mixture during the first-round PCR. The feasibility of the principle was demonstrated using a semi-nested primer system for the PCR analysis of genomic DNA. The first-round PCR reaction mixture was loaded into the capillary and covered by oil. Then, the second-round PCR reaction mixture was layered on top of it. PCR was run in two rounds separated by a centrifugation step that combined the second-round PCR mixture with the first-round products. Amplified products were visualized by fluorescence melting curve analysis. RESULTS: When a dilution series of genomic DNA was used for the single-capillary two-round PCR, 0.1 ng of DNA could consistently be detected. This was a 10-fold increase of sensitivity in comparison with single-round PCR. With the new technique, the first-round reaction mixture was sufficiently separated from second-round primers by the oil layer. CONCLUSIONS: Two-round PCR on the LightCycler using a single closed capillary excluded the possibility of amplification product carry-over. This new technique can easily be adapted for numerous applications, and should show feasibility for many nested primer PCR applications currently in use to the clinical detection of virus-derived DNA.

DNA↗
PubMed1994

[Atypical presentation of Leber's optic neuropathy].

BACKGROUND: Leber's optic neuropathy (LON) is the phenotypic expression of an inherited disorder due to a mitochondrial DNA mutation. Numerous loci of a point mutation in the mitochondrial genome are reported: 3460, 4160, 11778, 14484 and, 15257. Typically visual loss occurs in young males and a positive family history is found. Peripapillary telangiectasias are reported to be diagnostic for the disease and cardiac conduction abnormalities are sometimes present. PATIENTS: We present six patients who lost vision in both eyes with neither family history of visual loss, typical fundus abnormalities, nor cardiac abnormalities. All were initially misdiagnosed as either anterior ischemic optic neuropathy, hereditary optic atrophy, thromboembolic disorder, toxic amblyopia, multiple sclerosis, traumatic optic neuropathy, or complicated papilledema. METHODS AND RESULTS: Diagnosis was possible in all six cases by mitochondrial DNA studies (five patients with 11778, one with 3460). Magnetic resonance imaging using short-time inversion recovery sequences demonstrated in three tested patients a hyperintense signal within the intraorbital portion of the optic nerve, enhancing after Gadolinium infusion. CONCLUSION: Presentation of LON can be atypical, i.e. occurring in a female, at an advanced age, without family history, without retinal telangiectasias, with other fundus findings, or with unilateral visual loss for prolonged period. Diagnosis of LON should be suspected in every patient with atypical visual loss secondary to an optic neuropathy of undetermined etiology and mitochondrial DNA studies should be performed. Magnetic resonance imaging can be helpful in such cases.

Adult↗
PubMed1995

A behavioral screen for isolating zebrafish mutants with visual system defects.

Optokinetic and phototactic behaviors of zebrafish larvae were examined for their usefulness in screening for recessive defects in the visual system. The optokinetic response can be reliably and rapidly detected in 5-day larvae, whereas the phototactic response of larvae is variable and not robust enough to be useful for screening. We therefore measured optokinetic responses of mutagenized larvae as a genetic screen for visual system defects. Third-generation larvae, representing 266 mutagenized genomes, were examined for abnormal optokinetic responses. Eighteen optokinetic-defective mutants were identified and two mutants that did not show obvious morphological defects, no optokinetic response a (noa) and partial optokinetic response a (poa), were studied further. We recorded the electroretinogram (ERG) to determine whether these two mutations affect the retina. The b-wave of noa larvae was grossly abnormal, being delayed in onset and significantly reduced in amplitude. In contrast, the ERG waveform of poa larvae was normal, although the b-wave was reduced in amplitude in bright light. Histologically, the retinas of noa and poa larvae appeared normal. We conclude that noa larvae have a functional defect in the outer retina, whereas the outer retina of poa larvae is likely to be normal.

Animals↗
PubMed2002

EB1 targets to kinetochores with attached, polymerizing microtubules.

Microtubule polymerization dynamics at kinetochores is coupled to chromosome movements, but its regulation there is poorly understood. The plus end tracking protein EB1 is required both for regulating microtubule dynamics and for maintaining a euploid genome. To address the role of EB1 in aneuploidy, we visualized its targeting in mitotic PtK1 cells. Fluorescent EB1, which localized to polymerizing ends of astral and spindle microtubules, was used to track their polymerization. EB1 also associated with a subset of attached kinetochores in late prometaphase and metaphase, and rarely in anaphase. Localization occurred in a narrow crescent, concave toward the centromere, consistent with targeting to the microtubule plus end-kinetochore interface. EB1 did not localize to kinetochores lacking attached kinetochore microtubules in prophase or early prometaphase, or upon nocodazole treatment. By time lapse, EB1 specifically targeted to kinetochores moving antipoleward, coupled to microtubule plus end polymerization, and not during plus end depolymerization. It localized independently of spindle bipolarity, the spindle checkpoint, and dynein/dynactin function. EB1 is the first protein whose targeting reflects kinetochore directionality, unlike other plus end tracking proteins that show enhanced kinetochore binding in the absence of microtubules. Our results suggest EB1 may modulate kinetochore microtubule polymerization and/or attachment.

Cell Nucleus↗
PubMed2003

The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.

Arabidopsis thaliana is the most widely-studied plant today. The concerted efforts of over 11 000 researchers and 4000 organizations around the world are generating a rich diversity and quantity of information and materials. This information is made available through a comprehensive on-line resource called the Arabidopsis Information Resource (TAIR) (http://arabidopsis.org), which is accessible via commonly used web browsers and can be searched and downloaded in a number of ways. In the last two years, efforts have been focused on increasing data content and diversity, functionally annotating genes and gene products with controlled vocabularies, and improving data retrieval, analysis and visualization tools. New information include sequence polymorphisms including alleles, germplasms and phenotypes, Gene Ontology annotations, gene families, protein information, metabolic pathways, gene expression data from microarray experiments and seed and DNA stocks. New data visualization and analysis tools include SeqViewer, which interactively displays the genome from the whole chromosome down to 10 kb of nucleotide sequence and AraCyc, a metabolic pathway database and map tool that allows overlaying expression data onto the pathway diagrams. Finally, we have recently incorporated seed and DNA stock information from the Arabidopsis Biological Resource Center (ABRC) and implemented a shopping-cart style on-line ordering system.

Arabidopsis↗
PubMed2007

Opsin gene duplication and diversification in the guppy, a model for sexual selection.

Identification of genes that control variation in adaptive characters is a prerequisite for understanding the processes that drive sexual and natural selection. Male coloration and female colour perception play important roles in mate choice in the guppy (Poecilia reticulata), a model organism for studies of natural and sexual selection. We examined a potential source for the known variation in colour perception, by analysing genomic and complementary DNA sequences of genes that code for visual pigment proteins. We find high sequence variability, both within and between populations, and expanded copy number for long-wave sensitive (LWS) opsin genes. Alleles with non-synonymous changes that suggest dissimilar spectral tuning properties occur in the same population and even in the same individual, and the high frequency of non-synonymous substitutions argues for diversifying selection acting on these proteins. Therefore, variability in tuning amino acids is partitioned within individuals and populations of the guppy, in contrast to variability for LWS at higher taxonomic levels in cichlids, a second model system for differentiation owing to sexual selection. Since opsin variability parallels the extreme male colour polymorphism within guppy populations, we suggest that mate choice has been a major factor driving the coevolution of opsins and male ornaments in this species.

Alleles↗
PubMed2025

Detection of Orsay viral replication intermediates reveals spatial and regulatory links to Caenorhabditis elegans innate immune responses.

For a positive-strand RNA virus, the encoded viral RNA-dependent RNA polymerase (oRdRP) synthesizes complementary antigenome strand and uses it as a template for amplifying the viral genome, generating various replication intermediates. Structural proteins and viral genome are packaged into virions, but the fate of replication intermediates is underexplored. Here, we investigate Orsay Virus (OV) replication intermediates, including antigenome, oRdRP and double stranded RNA (dsRNA), using PCR and fluorescence-based imaging in C. elegans intestines. As for other positive-strand RNA viruses, we find that genome is in vast excess of antigenome. Antigenome is only visualized in cells when using denaturation protocols, indicating basepaired intermediates. OV antigenome is observed with distinct cytoplasmic and perinuclear localization patterns that depend on factors required for generation of primary, but not secondary, siRNAs. In both wildtype and RNA interference (RNAi) mutants, viral dsRNA is observed in the cytoplasm associated with oRdRP, suggesting cytoplasmic virus replication hubs. Additionally, using antibodies to oRdRP, we observed spherical structures of ~1μm in diameter defined by oRdRP at their surface; over 75% of infected wildtype animals show these structures, which associate with mitochondria and autophagosomes in an antiviral RNAi- and autophagy-dependent manner, respectively. Our study defines new features of OV replication intermediates in wildtype animals, setting the stage for understanding their connection to the viral life cycle and host antiviral pathways.

Journal Article↗
PubMed1991

Multiple basal promoter elements determine the level of human c-fos transcription.

Three cis-acting domains that contribute to the basal promoter activity of the human c-fos gene were identified. One encompasses the serum response element and has been previously described. Another spans an NF1-like site situated at -170. Mutations and in vitro protein binding assays pinpoint this site as the sole basal element of the medial domain. The third, or promoter-proximal, domain can be divided into several distinct sites, one containing a directly repeated GC-rich element and the other consisting of partially overlapping recognition sites for transcription factors ATF/CREB and MLTF/USF. Each of these sites contributes to basal activity as assayed by transient transfections and by in vitro transcription. Consistent with this, several complexes could be visualized between this region and nuclear proteins in vitro and genomic footprinting demonstrated that both elements are constitutively bound in vivo. On the basis of these results, we conclude that all three domains are necessary for full c-fos promoter function.

Base Sequence↗
PubMed2004

In vivo DNA deletion assay to detect environmental and genetic predisposition to cancer.

Large-scale genomic rearrangements such as DNA deletions play a role in the etiology of cancer. The frequency of DNA deletions can be elevated by exposure to carcinogens or by mutations in genes involved in the maintenance of genomic integrity. The in vivo DNA deletion assay allows a visual detection of deletion events within the pink-eyed unstable (pun) locus in developing mouse embryos. A deletion of one copy of a duplicated 70-kb DNA fragment within the pun locus restores the pink-eyed dilute (p) gene, which encodes a protein responsible for the assembly of a black color melanin complex. Deletion events occurring in premelanocytes cause visible black patches (fur-spots) on the light gray fur of offspring and black pigmented cells (eye-spots) on the unpigmented retinal pigment epithelium (RPE). In the fur-spot assay, 10-d-old pups are observed for black spots on the fur. In the eye-spot assay, mice are sacrificed at d 20, eyes are removed, and the wholemount RPE slides are prepared for eye-spot analysis. The frequency, size, and position relative to the optic nerve of the eye-spots are determined. This assay can be used to study the effect of environmental chemicals and physical agents as well as the genetic control of DNA deletions in vivo.

Animals↗
PubMed2002

Fluorescence in situ hybridization (FISH) in the molecular cytogenetics of cancer.

In this review, we discuss the developments of fluorescence in situ hybridization (FISH) and place them in the context of their applications in cancer research. These methods are not only very useful for the causal analysis of the development and spread of certain tumors, they are also efficient tools for tumor diagnosis. Although a review of all of the literature in this field is not possible here, many of the major contributions are summarized along with recent work from our laboratory. Our group contributes to the goal of functional identification of tumor growth antagonizing genes. FISH and molecular analyses have shown that the short arm of human chromosome 3 is frequently deleted in kidney, lung, breast, uterus, testis and ovary carcinomas. Deletion-mapping studies have outlined several separate deletion prone regions in different tumors, namely 3pter-p25, p22-p21.3, p21.1-p14 and p14-p12, which may contain putative tumor suppressor genes (TSGs). Candidate suppressor genes isolated from frequently deleted regions need to be assayed for possible tumor-antagonizing ability by functional tests. We have developed a functional test system, the microcell hybrid (MCH) based "elimination test" (Et). The Et is based on the introduction of a single human chromosome into tumor cells of human or murine origin, via microcell fusion. The MCHs were analyzed by FISH painting and PCR for the elimination or retention of specific human chromosome 3 (chr. 3) regions after one or several passages in severe combined immunedeficient (SCID) mice. We have defined a common eliminated region (CER) on chr. 3p21.3. CER is approximately 1 megabase (Mb) in size. We have covered this region with PACs (bacteriophage PI based artificial chromosome) and used FISH mapping for localization and ordering PACs and cosmids on the chromosome 3 and high-resolution free chromatin/DNA fiber FISH to orient the PAC contig, to measure the lengths of PACs, and to establish their order. Activation of cellular oncogene by chromosomal tanslocation, which brings an oncogene under the influence of a highly active chromosome region, appears to play a pivotal role in the genesis of certain hematopoetic and lymphoid tumors. We have detected specific chromosomal translocations by FISH painting in mouse plamacytoma (MPC), human Burkitt lymphoma (BL) other B-cell derived tumors. We have showed in a murine sarcoma derived line (SEWA) that FISH can be also be used for detection of amplified oncogene (c-myc) and the linked locus (pvt-1). We have also applied the FISH technique for visualization of integrated and episomal Epstein-Barr virus (EBV) genomes and EBV transcripts in EBV-carrying B-cell derived human cell lines.

Cytogenetic Analysis↗
PubMed1994

Archaebacterial ether-linked lipid biosynthetic gene. Expression cloning, sequencing, and characterization of geranylgeranyl-diphosphate synthase.

Archaebacterial Sulfolobus acidocaldarius geranylgeranyl-diphosphate (GGPP) synthase (EC 2.5.1.29) catalyzes consecutive condensations of isopentenyl diphosphate with allylic diphosphates to produce GGPP which is the important precursor of archaebacterial ether-linked lipids. We developed an expression screening method for cloning the GGPP synthase gene, which utilizes the carotenoid biosynthesis genes of Erwinia uredovora to visualize a clone expressing GGPP synthase, and then screened a genomic DNA library from S. acidocaldarius for the GGPP synthase gene by using this method. Positive clones were shown to contain GGPP synthase gene by the use of an in vitro assay. Extracts from Escherichia coli transformants catalyzed the condensation of isopentenyl diphosphate with farnesyl diphosphate (FPP) to produce (all-E)-GGPP. The nucleotide sequence of the 2.3-kilobase HindIII fragment of the cloned fragment was determined. This sequence specifies two open reading frames, ORF-1 and ORF-2. ORF-1 encodes GGPP synthase with the expected molecular weight of 36,873, and ORF-2 encodes a protein with homology for UDP-N-acetylglucosaminedolichyl phosphate N-acetylglucosaminephosphotransferase. The cloned GGPP synthase was partially purified with several chromatographies after heat treatment of cell free extract. This enzyme is extremely thermostable and has an optimal pH at 5.8. Dimethylallyl diphosphate, geranyl diphosphate, and (all-E)-FPP are, in decreasing order of activity, acceptable as allylic substrates to produce (all-E)-GGPP. When dimethylallyl diphosphate or geranyl diphosphate are the allylic substrates, a significant amount of mixture of the products is shorter than GGPP. (2Z,6E)-FPP is not a substrate. This enzyme recognizes the E-configuration of allylic substrate.

Alkyl and Aryl Transferases↗
PubMedDate not supplied

[Vitamin D induces proliferation in rat endometrium cultured cells].

OBJECTIVE: To study the effects of 1,25-dihydroxyvitaminD3 (1,25-(OH)2D3) on proliferation and cell death in the rat uterus. MATERIAL AND METHODS: A rat endometrial cell line (Rentro 1) grown in a Dulbecco Minimal Essential Medium (DMEM) supplemented with 1% charcoal stripped serum was used in all experiments in order to eliminate the steroid hormone. Cell monolayer was incubated in the presence and absence of 1,25-(OH)2D3 or 17 beta-estradiol or vehicle. After stimulation, we evaluated cell proliferation and DNA synthesis by trypan blue counting method and flow cytofluorometry, respectively. Finally, the genomic DNA integrity was evaluated by electrophoresis and the bands visualized with ultraviolet light. RESULTS: The cells in medium containing 1% fetal bovine serum free of steroid hormones stimulated the cell growth 85% more than without serum. Supplement with albumin did not allow cell growth. The cells did not respond to 17 beta-estradiol but the presence of 1,25-(OH)2D3 induced cell proliferation. These results confirm that Rentro 1 cells do not express the estrogen receptor and demonstrate their capacity to respond to 1,25-(OH)2D3. Finally, the integrity of DNA was not affected by 1,25(OH)2D3, suggesting that this hormone is not involved in cell death by apoptosis in our cell line, as seen in other cell lines. CONCLUSIONS: 1) 1,25-dihydroxyvitamin D induced cell proliferation in the endometrial cell line Rentro 1 in a dose-dependent fashion and this effect is independent of the presence of an estrogenic stimulus; 2) the increase in cell number was related to DNA synthesis during the cell cycle; and 3) the presence of the hormone in the culture medium was not able to induce cell death.

Animals↗
PubMed1995

A single gel analysis of 575 dominant and codominant restriction landmark genomic scanning loci in mice interspecific backcross progeny.

We identified 575 new NotI landmarks of C57BL/6(B)- and M. spretus (S)-specific, dominant and codominant loci which were segregated in B x S interspecific backcrosses (BSS), using the restriction landmark genomic scanning (RLGS) spot mapping method. All of these loci were visualized on a single RLGS profile which was produced with NotI-PvuII-PstI. These landmarks include 250 newly identified S-specific spots in addition to the previously reported 325 B-specific spots. The S-specific spots were identified by reading full or half intensity, based on the property that the spot intensity of the autoradiographic signal reflected the copy number of an end-labeled restriction landmark. The cumulative map is 1341 cM and it is based upon 985 meiotic events in 72 backcross progeny. This map covers 90% of the total estimated length of the mouse genetic map. This map provides a good tool for the high-speed genome scanning assay in the mouse genome by a single RLGS gel analysis.

Animals↗
PubMed2003

Genomic characterization of Rim2/Hipa elements reveals a CACTA-like transposon superfamily with unique features in the rice genome.

The availability of huge amounts of rice genome sequence now permits large-scale analysis of the structure and molecular characteristics of the previously identified transposase-encoding Rim2 (also called Hipa) element, which is transcriptionally activated by infection with the fungal pathogen Magnaporthe grisea and by treatment with the corresponding fungal elicitor. Based on genomic cloning and data mining from 230 Mb of rice genome sequence, 347 Rim2 elements, with an average size of 5.8 kb, were identified. This indicates that an estimated total of 600-700 Rim2 elements are present in the whole genome. Rim2 insertions occur non-randomly on the chromosomes, as visualized by fluorescence in situ hybridization. The elements harbor 16-bp terminal inverted repeats with the core sequence CACTG, 16-bp sub-terminal repeats, internal variable regions, 3-bp target sequence duplications in the flanking regions, and genes coding for Rim2 proteins (the putative transposase) and hydroxyproline-rich glycoproteins. High levels of insertion into genic regions are observed for members of this family, and the transposition history of the family can be deduced from the high level of shared sequences and analysis of repeat target sites of the elements. Phylogenetic analysis indicates that the putative RIM2 proteins fall into a subgroup distinct from the TNP2-like subgroup of transposases. Southern hybridization with genomic DNA from monocotyledonous and dicotyledonous plants demonstrates that the RIM2-coding sequence is unique to the Oryza genome. Our results demonstrate that the Rim2 elements from rice belong to a distinct superfamily of CACTA-like elements with evolutionary diversity.

Amino Acid Sequence↗
PubMed2005

Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data.

BACKGROUND: The identification of disease-associated genes using single nucleotide polymorphisms (SNPs) has been increasingly reported. In particular, the Affymetrix Mapping 10 K SNP microarray platform uses one PCR primer to amplify the DNA samples and determine the genotype of more than 10,000 SNPs in the human genome. This provides the opportunity for large scale, rapid and cost-effective genotyping assays for linkage analysis. However, the analysis of such datasets is nontrivial because of the large number of markers, and visualizing the linkage scores in the context of genome maps remains less automated using the current linkage analysis software packages. For example, the haplotyping results are commonly represented in the text format. RESULTS: Here we report the development of a novel software tool called CompareLinkage for automated formatting of the Affymetrix Mapping 10 K genotype data into the "Linkage" format and the subsequent analysis with multi-point linkage software programs such as Merlin and Allegro. The new software has the ability to visualize the results for all these programs in dChip in the context of genome annotations and cytoband information. In addition we implemented a variant of the Lander-Green algorithm in the dChipLinkage module of dChip software (V1.3) to perform parametric linkage analysis and haplotyping of SNP array data. These functions are integrated with the existing modules of dChip to visualize SNP genotype data together with LOD score curves. We have analyzed three families with recessive and dominant diseases using the new software programs and the comparison results are presented and discussed. CONCLUSIONS: The CompareLinkage and dChipLinkage software packages are freely available. They provide the visualization tools for high-density oligonucleotide SNP array data, as well as the automated functions for formatting SNP array data for the linkage analysis programs Merlin and Allegro and calling these programs for linkage analysis. The results can be visualized in dChip in the context of genes and cytobands. In addition, a variant of the Lander-Green algorithm is provided that allows parametric linkage analysis and haplotyping.

Family Health↗
PubMed2000

Expression profile viewer (ExProView): a software tool for transcriptome analysis.

A software tool, Expression Profile Viewer (ExProView), for analysis of gene expression profiles derived from expressed sequence tags (ESTs) and SAGE (serial analysis of gene expression) is presented. The software visualizes a complete set of classified transcript data in a two-dimensional array of dots, a "virtual chip," in which each dot represents a known gene as characterized in the transcript databases Expressed Gene Anatomy Database or UniGene. The virtual chip display can be changed between representations of different conceptual systems for gene/protein classification and grouping. Four alternative projections are currently available: (i) cellular role, (ii) subcellular compartment, (iii) chromosome localization, and (iv) total UniGene display. However, the chip can be adapted to any other desired layout. By selecting dots, further information about the represented genes is obtained from the local database and WWW links. The software thus provides a visualization of global mRNA expression at the descriptive level and guides in the exploration of patterns of functional expression, while maintaining direct access to detailed information on each individual gene. To evaluate the software, public EST and SAGE gene expression data obtained from the Cancer Genome Anatomy Project at the National Center for Biotechnology Information were analyzed and visualized. A demonstration of the software is available at http://www.biochem.kth. se/exproview/.

Data Display↗