Biomedical subjects

Naomi Rosen

Publications and source records attributed to Naomi Rosen.

5 recordsLinked to original sources

PubMed2004

GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes.

MOTIVATION: High density oligonucleotide arrays are usually annotated in a one-to-one fashion, with each probeset assigned to one gene. However, in reality, subsets of oligonucleotides in a probeset may match sequences within more than one gene, potentially leading to misinterpretations. Moreover, a gene is often represented by more than one probeset, and analyzing probe matches at the mRNA level can help one deduce whether these probesets are derived from the same or different splice variants. RESULTS: The GeneAnnot system comprehensively documents the many-to-many relationship between oligonucleotide array probesets and annotated genes in GeneCards. It performs pairwise alignments between the probe sequences and gene transcripts, and assigns sensitivity and specificity scores to each probeset/gene pair. AVAILABILITY: http://genecards.weizmann.ac.il/geneannot/ SUPPLEMENTARY INFORMATION: Program description and statistics http://genecards.weizmann.ac.il/geneannot/DOC/index.html

Algorithms↗

PubMed2003

Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE.

Recent enhancements and current research in the GeneCards (GC) (http://bioinfo.weizmann.ac.il/cards/) project are described, including the addition of gene expression profiles and integrated gene locations. Also highlighted are the contributions of specialized associated human gene-centric databases developed at the Weizmann Institute. These include the Unified Database (UDB) (http://bioinfo.weizmann.ac.il/udb) for human genome mapping, the human Chromosome 21 database at the Weizmann Insti-tute (CroW 21) (http://bioinfo.weizmann.ac.il/crow21), and the Human Olfactory Receptor Data Explora-torium (HORDE) (http://bioinfo.weizmann.ac.il/HORDE). The synergistic relationships amongst these efforts have positively impacted the quality, quantity and usefulness of the GeneCards gene compendium.

Algorithms↗

PubMed2003

GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia.

The interpretation of microarray expression results often includes extensive efforts to identify and annotate the gene representatives immobilised on the arrays. In this paper we describe the usage of our automatic GeneAnnot system, which links between Affymetrix arrays and the rich human gene annotations available in GeneCards. We explain GeneCards search options and results display; elaborate on the presentation of expression information in GeneCards, including both our whole-genome GeneNote project and external expression resources; describe the various parameters and displays used by GeneAnnot to assess the annotation quality and probeset specificity; and show how to search GeneAnnot and GeneNote websites directly.

Data Interpretation, Statistical↗

PubMed2003

GeneLoc: exon-based integration of human genome maps.

MOTIVATION: Despite the numerous available whole-genome mapping resources, no comprehensive, integrated map of the human genome yet exists. RESULTS: GeneLoc, software adjunct to GeneCards and UDB, integrates gene lists by comparing genomic coordinates at the exon level and assigns unique and meaningful identifiers to each gene.

Chromosome Mapping↗

PubMed2002

GeneCards 2002: towards a complete, object-oriented, human gene compendium.

MOTIVATION: In the post-genomic era, functional analysis of genes requires a sophisticated interdisciplinary arsenal. Comprehensive resources are challenged to provide consistently improving, state-of-the-art tools. RESULTS: GeneCards (Rebhan et al., 1998) has made innovative strides: (a). regular updates and enhancements incorporating new genes enriched with sequences, genomic locations, cDNA assemblies, orthologies, medical information, 3D protein structures, gene expression, and focused SNP summaries; (b). restructured software using object-oriented Perl, migration to schema-driven XML, and (c). pilot studies, introducing methods to produce cards for novel and predicted genes.

Algorithms↗