ABSTRACT
In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap'99, Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri-tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov.
Subject(s)
Biotechnology , Databases, Factual , Information Services , Animals , Gene Expression Profiling , Genome , Genome, Human , Humans , Information Storage and Retrieval , Internet , Molecular Biology , National Institutes of Health (U.S.) , National Library of Medicine (U.S.) , Phenotype , Sequence Alignment , United StatesABSTRACT
We have constructed a public gene expression data repository and online data access and analysis, WWW and FTP sites for serial analysis of gene expression (SAGE) data. The WWW and FTP components of this resource, SAGEmap, are located at http://www.ncbi.nlm.nih. gov/sage and ftp://ncbi.nlm.nih.gov/pub/sage, respectively. We herein describe SAGE data submission procedures, the construction and characteristics of SAGE tags to gene assignments, the derivation and use of a novel statistical test designed specifically for differential-type analyses of SAGE data, and the organization and use of this resource.
Subject(s)
Databases, Factual , Gene Expression/genetics , Internet , Female , Gene Library , Humans , Male , Sequence Analysis, DNA/methods , Sequence Tagged Sites , Signal Processing, Computer-AssistedSubject(s)
Cytogenetic Analysis , Genome, Human , Human Genome Project , Physical Chromosome Mapping/methods , Chromosomes, Bacterial/genetics , Chromosomes, Human, Pair 22/genetics , Chromosomes, Human, Pair 7/genetics , Cloning, Molecular , Contig Mapping , Humans , In Situ Hybridization, Fluorescence , Sequence Tagged SitesSubject(s)
Gene Expression Profiling/methods , Prostatic Neoplasms/genetics , Databases, Factual , Gene Expression , Gene Expression Profiling/statistics & numerical data , Gene Library , Humans , Male , Oligonucleotide Array Sequence Analysis , Pathology, Clinical/methods , Polymorphism, Single NucleotideABSTRACT
In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval and resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing pages, GeneMap'99, Davis Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP) pages, Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP) pages, SAGEmap, Online Mendelian Inheritance in Man (OMIM) and the Molecular Modeling Database (MMDB). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov
Subject(s)
Biology , Databases, Factual , Animals , Gene Expression , Genome, Human , Humans , Information Storage and Retrieval , Mice , Models, Molecular , National Library of Medicine (U.S.) , Neoplasms/genetics , Phenotype , United StatesABSTRACT
A public database, SAGEmap, was created as a component of the Cancer Genome Anatomy Project to provide a central location for depositing, retrieving, and analyzing human gene expression data. This database uses serial analysis of gene expression to quantify transcript levels in both malignant and normal human tissues. By accessing SAGEmap (http://www.ncbi.nlm.nih.gov/SAGE) the user can compare transcript populations between any of the posted libraries. As an initial demonstration of the database's utility, gene expression in human glioblastomas was compared with that of normal brain white matter. Of the 47,174 unique transcripts expressed in these two tissues, 471 (1.0%) were differentially expressed by more than 5-fold (P<0.001). Classification of these genes revealed functions consistent with the biological properties of glioblastomas, in particular: angiogenesis, transcription, and cell cycle related genes.
Subject(s)
Databases, Factual , Gene Expression , Neoplasms/genetics , Brain/metabolism , Cloning, Molecular , Glioblastoma/genetics , Humans , Internet , Models, Theoretical , RNA, Messenger/analysis , Reverse Transcriptase Polymerase Chain Reaction , Tissue DistributionSubject(s)
Gene Expression , Colorectal Neoplasms/genetics , Female , Genome, Human , Humans , Male , Neoplasms/genetics , Tissue Distribution , Tumor Cells, CulturedABSTRACT
Identification of loss of heterozygosity (LOH) at specific genetic loci in cancer cells suggests the presence of a tumor suppressor gene within the deleted region. A basal cell carcinoma (BCC) susceptibility gene, human homolog of drosophila patched (PTC), has been recently cloned and localized on chromosome 9q22.3. Mutation and deletion of this region has been reported in BCCs using frozen tumor tissue. The objective of this study was to test whether LOH of human PTC on chromosome 9q22 could be detected in archival sporadic BCCs. We studied 20 randomly selected sporadic BCCs by microdissection and polymerase chain reaction using paraffin-embedded, formalin-fixed material on glass slides. In all cases, analysis was performed with the polymorphic markers D9S53, D9S15, D9S287, and D9S303. The LOH frequencies were 30%, 42%, 56%, and 75% with D9S15, D9S287, D9S53, and D9S303, respectively. LOH at 9q22 was identified in 12 of 20 cases (60%) with at least one marker. Seven cases showed LOH with two markers, two cases with three markers, and one case showed LOH with all four markers. The results indicate that BCC LOH can be frequently identified in paraffin-embedded BCC after routine processing.
Subject(s)
Carcinoma, Basal Cell/genetics , Chromosomes, Human, Pair 9 , Skin Neoplasms/genetics , Aged , Aged, 80 and over , Humans , Loss of Heterozygosity , Male , Membrane Proteins/genetics , Patched Receptors , Receptors, Cell SurfaceABSTRACT
BACKGROUND: In young children and infants, Wilms' tumor is the most common cancer of the kidney. Wilms' tumor exhibits heterogeneous histopathologic features, consisting of rapidly proliferating blastemal and epithelial cells and a stromal component that has heterologous elements (e.g., cartilage, bone, and striated muscle). It is unclear whether the stromal and heterologous components of sporadic Wilms' tumor are neoplastic or should be considered non-neoplastic. PURPOSE: Our purpose was twofold: 1) to selectively analyze the different histologic tissue components of sporadic Wilms' tumors, including blastemal, epithelial, stromal, and heterologous elements, for loss of heterozygosity (LOH) of the WT1 gene and for expression of the WT1 gene and 2) to determine the role of WT1 gene expression in the development of these tissues. METHODS: By use of tissue microdissection techniques, various histologic elements (blastema, stroma, epithelium, and striated muscle) of sporadic Wilms' tumor were obtained from specimens taken from 18 patients. DNA was extracted from the dissected tissue fragments, and DNA solutions were amplified by use of the polymerase chain reaction and the polymorphic genomic markers D11S1392 and D11S904 to detect LOH at the WT1 gene locus (11p13). Three selected specimens with heterologous elements and LOH at 11p13 were analyzed for expression of the WT1 gene by means of the in situ reverse transcription-polymerase chain reaction. RESULTS: Nine (50%) of the 18 specimens showed LOH at the WT1 locus. Although identical WT1 gene deletion was consistently observed in all of the various histologic components of these nine specimens, WT1 gene expression was high in the blastemal and epithelial elements and low in the stromal and heterologous elements. CONCLUSIONS AND IMPLICATIONS: Identical allelic deletion at 11p13 in all components of the sporadic Wilms' tumors examined suggests that the stromal tissue components are neoplastic rather than non-neoplastic. In conjunction with variable WT1 gene expression in the different histologic components, the results raise the possibility that undifferentiated blastemal cells are the precursors of the stromal and heterologous elements. Morphologically benign stromal and heterologous elements may therefore be derived from neoplastic cells. The developmental state of the various tissue components of Wilms' tumor may be attributed to an altered residual WT1 gene that is required for the maturation of blastemal and epithelial cells but that is not required for the maturation of stromal and heterologous elements.
Subject(s)
Chromosome Deletion , Gene Deletion , Gene Expression Regulation, Neoplastic , Genes, Wilms Tumor , Kidney Neoplasms/genetics , Wilms Tumor/genetics , Alleles , DNA Probes , Heterozygote , Humans , Kidney Neoplasms/pathology , Polymerase Chain Reaction/methods , Transcription, Genetic , Wilms Tumor/pathologyABSTRACT
About 10% of patients with renal cancer develop tumor thrombus. Rapid extension of the tumor thrombus with clot is rare. We report a case of rapidly progressing tumor thrombus complicated by massive pulmonary embolus.
