LINADMIX: evaluating the effect of ancient admixture events on modern populations.

Motivation: The rise in the number of genotyped ancient individuals provides an opportunity to estimate population admixture models for many populations. However, in models describing modern populations as mixtures of ancient ones, it is typically difficult to estimate the model mixing coefficients and to evaluate its fit to the data.

Results: We present LINADMIX, designed to tackle this problem by solving a constrained linear model when both the ancient and the modern genotypes are represented in a low-dimensional space.

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards.

Unlabelled: A major challenge in understanding gene regulation is the unequivocal identification of enhancer elements and uncovering their connections to genes. We present GeneHancer, a novel database of human enhancers and their inferred target genes, in the framework of GeneCards. First, we integrated a total of 434 000 reported enhancers from four different genome-wide databases: the Encyclopedia of DNA Elements (ENCODE), the Ensembl regulatory build, the functional annotation of the mammalian genome (FANTOM) project and the VISTA Enhancer Browser.

The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.

GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools.

Non-redundant compendium of human ncRNA genes in GeneCards.

Motivation: Non-coding RNA (ncRNA) genes are increasingly acknowledged for their importance in the human genome. However, there is no comprehensive non-redundant database for all such human genes.

Results: We leveraged the effective platform of GeneCards, the human gene compendium, together with the power of fRNAdb and additional primary sources, to judiciously unify all ncRNA gene entries obtainable from 15 different primary sources.

In-silico human genomics with GeneCards.

Since 1998, the bioinformatics, systems biology, genomics and medical communities have enjoyed a synergistic relationship with the GeneCards database of human genes (http://www.genecards.org).

GeneCards Version 3: the human gene integrator.

GeneCards (www.genecards.org) is a comprehensive, authoritative compendium of annotative information about human genes, widely used for nearly 15 years.

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.

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.

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.

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.

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.