GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation.

@article{Stelzer2009GeneDecksPH,
  title={GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation.},
  author={Gil Stelzer and Aron Inger and Tsviya Olender and Tsippi Iny-Stein and Irina Dalah and Arye Harel and Marilyn Safran and Doron Lancet},
  journal={Omics : a journal of integrative biology},
  year={2009},
  volume={13 6},
  pages={
          477-87
        }
}
Sophisticated genomic navigation strongly benefits from a capacity to establish a similarity metric among genes. GeneDecks is a novel analysis tool that provides such a metric by highlighting shared descriptors between pairs of genes, based on the rich annotation within the GeneCards compendium of human genes. The current implementation addresses information about pathways, protein domains, Gene Ontology (GO) terms, mouse phenotypes, mRNA expression patterns, disorders, drug relationships, and… 

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References

SHOWING 1-10 OF 46 REFERENCES

GIFtS: annotation landscape analysis with GeneCards

GIFtS can be a valuable tool for computational procedures which analyze lists of large set of genes resulting from wet-lab or computational research, and may also assist the scientific community with identification of groups of uncharacterized genes for diverse applications, such as delineation of novel functions and charting unexplored areas of the human genome.

In-silico human genomics with GeneCards

The evolution and architecture of this project is described, including examples of synergistic applications in diverse areas such as synthetic lethality in cancer, the annotation of genetic variations in disease, omics integration in a systems biology approach to kidney disease, and bioinformatics tools.

FunSimMat: a comprehensive functional similarity database

FunSimMat is described, a large new database that provides several different semantic similarity measures for GO terms and offers various precomputed functional similarity values for proteins contained in UniProtKB and for protein families in Pfam and SMART.

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

Recent enhancements and current research in the GeneCards project are described, including the addition of gene expression profiles and integrated gene locations and the contributions of specialized associated human gene-centric databases developed at the Weizmann Institute.

Judging the quality of gene expression-based clustering methods using gene annotation.

It is concluded that enrichment of clusters for biological function is, in general, highest at rather low cluster numbers, and no method outperforms Euclidean distance for ratio-based measurements, or Pearson distance at the optimal choice of cluster number.

Gene Ontology: tool for the unification of biology

The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification

The analyses provide a novel route to infer expression profiles for presumed ancestral nodes in the tissue dendrogram, whereby de novo enhancement and diminution of gene expression go hand in hand, and highlight the importance of gene suppression events.

Gene Ontology annotation quality analysis in model eukaryotes

The GO Annotation Quality (GAQ) score is reported, a quantitative measure of GO quality that includes breadth of GO annotation, the level of detail of annotation and the type of evidence used to make the annotation.

NetAffx: Affymetrix probesets and annotations

NetAffx details and annotates probesets on Affymetrix GeneChip microarrays, and lists the probe sequences, and the consensus sequence interrogated by the probes; for the larger chip sets, interactive maps display this sequence data in genomic context.