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… 
GIFtS: annotation landscape analysis with GeneCards
TLDR
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.
GeneCards Version 3: the human gene integrator
TLDR
A key focus is on gene-set analyses, which leverage GeneCards’ unique wealth of combinatorial annotations, which address a host of applications, including microarray data analysis, cross-database annotation mapping and gene-disorder associations for drug targeting.
Database update GeneCards Version 3: the human gene integrator
TLDR
A key focus is on gene-set analyses, which leverage GeneCards’ unique wealth of combinatorial annotations, which address a host of applications, including microarray data analysis, cross-database annotation mapping and gene-disorder associations for drug targeting.
In-silico human genomics with GeneCards
TLDR
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.
The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses
TLDR
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 and provides a stronger foundation for the GeneCards suite of companion databases and analysis tools.
Genic insights from integrated human proteomics in GeneCards
TLDR
The application of recent advances in proteomics to enhance gene annotation and classification in GeneCards is reported and a new metric for finding functional partners complements eight others, including sharing of pathways, gene ontology (GO) terms and domains, implemented in theGeneCards Suite.
ConceptGen: a gene set enrichment and gene set relation mapping tool
TLDR
ConceptGen, a web-based gene set enrichment and gene set relation mapping tool that is streamlined and simple to use, is developed and demonstrates the functionalities of ConceptGen using gene expression data modeling TGF-beta-induced epithelial-mesenchymal transition and metabolomics data comparing metastatic versus localized prostate cancers.
In-silico human genomics with
TLDR
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.
An Overview of Synergistic Data Tools for Biological Scrutiny
A network of biological databases is reviewed, supplying a framework for studies of human genes and the association of their genomic variations with human pheno- types. The network is composed of
The GeneCards Suite
The GeneCards® database of human genes was launched in 1997 and has expanded since then to encompass gene-centric, disease-centric, and pathway-centric entities and relationships within the GeneCards
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 47 REFERENCES
GIFtS: annotation landscape analysis with GeneCards
TLDR
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
TLDR
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.
AutoFACT: An Automatic Functional Annotation and Classification Tool
TLDR
This work presents AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence and determines the most informative functional description by combining multiple BLAST reports from several user-selected databases.
FunSimMat: a comprehensive functional similarity database
TLDR
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.
GOblet: a platform for Gene Ontology annotation of anonymous sequence data
TLDR
GOblet is a comprehensive web server application providing the annotation of anonymous sequence data with Gene Ontology (GO) terms and provides an improved display of results with the aid of Java applets.
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE
TLDR
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.
Characterization of protein-interaction networks in tumors
TLDR
Cancer PINs representing differentially regulated genes are larger than those of randomly selected protein lists, indicating functional dependencies among protein lists that can be identified on the basis of transcriptomics experiments, but the prevalence of hub proteins was not increased in the presence of cancer.
Judging the quality of gene expression-based clustering methods using gene annotation.
TLDR
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.
Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery.
TLDR
The challenges, research approaches and recently developed tools in the field of computational function-prediction are reviewed and the ways these issues can change the process of drug discovery are discussed.
Gene Ontology: tool for the unification of biology
TLDR
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.
...
1
2
3
4
5
...