In-silico Human Genomics with GeneCards

Overview

Journal Hum Genomics

Publisher Biomed Central

Specialty Genetics

Date 2011 Dec 14

PMID 22155609

Citations 117

Authors

Gil Stelzer

Irina Dalah

Tsippi Iny Stein

Yigeal Satanower

Naomi Rosen

Noam Nativ

Danit Oz-Levi

Tsviya Olender

Frida Belinky

Iris Bahir

Hagit Krug

Paul Perco

Bernd Mayer

Eugene Kolker

Marilyn Safran

Doron Lancet

Affiliations

Soon will be listed here.

Abstract

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). This human gene compendium was created to help to introduce order into the increasing chaos of information flow. As a consequence of viewing details and deep links related to specific genes, users have often requested enhanced capabilities, such that, over time, GeneCards has blossomed into a suite of tools (including GeneDecks, GeneALaCart, GeneLoc, GeneNote and GeneAnnot) for a variety of analyses of both single human genes and sets thereof. In this paper, we focus on inhouse and external research activities which have been enabled, enhanced, complemented and, in some cases, motivated by GeneCards. In turn, such interactions have often inspired and propelled improvements in GeneCards. We describe here the evolution and architecture of this project, 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.

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References

Bult C, Eppig J, Kadin J, Richardson J, Blake J . The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res. 2007; 36(Database issue):D724-8. PMC: 2238849. DOI: 10.1093/nar/gkm961. View

Alkharouf N, Jamison D, Matthews B . Online analytical processing (OLAP): a fast and effective data mining tool for gene expression databases. J Biomed Biotechnol. 2005; 2005(2):181-8. PMC: 1184053. DOI: 10.1155/JBB.2005.181. View

. The universal protein resource (UniProt). Nucleic Acids Res. 2007; 36(Database issue):D190-5. PMC: 2238893. DOI: 10.1093/nar/gkm895. View

Stelzer G, Inger A, Olender T, Iny-Stein T, Dalah I, Harel A . GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation. OMICS. 2009; 13(6):477-87. DOI: 10.1089/omi.2009.0069. View

Tarpey P, Smith R, Pleasance E, Whibley A, Edkins S, Hardy C . A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Nat Genet. 2009; 41(5):535-43. PMC: 2872007. DOI: 10.1038/ng.367. View

ORoak B, Deriziotis P, Lee C, Vives L, Schwartz J, Girirajan S . Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet. 2011; 43(6):585-9. PMC: 3115696. DOI: 10.1038/ng.835. View

Wright M, Bruford E . Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature. Hum Genomics. 2011; 5(2):90-8. PMC: 3051107. DOI: 10.1186/1479-7364-5-2-90. View

Sayers E, Barrett T, Benson D, Bolton E, Bryant S, Canese K . Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2010; 39(Database issue):D38-51. PMC: 3013733. DOI: 10.1093/nar/gkq1172. View

Barton G, Abbott J, Chiba N, Huang D, Huang Y, Krznaric M . EMAAS: an extensible grid-based rich internet application for microarray data analysis and management. BMC Bioinformatics. 2008; 9:493. PMC: 2615452. DOI: 10.1186/1471-2105-9-493. View

10.

Fechete R, Barth S, Olender T, Munteanu A, Bernthaler A, Inger A . Synthetic lethal hubs associated with vincristine resistant neuroblastoma. Mol Biosyst. 2010; 7(1):200-14. DOI: 10.1039/c0mb00082e. View

11.

Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M . Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics. 2007; 8:446. PMC: 2216044. DOI: 10.1186/1471-2105-8-446. View

12.

Fu N, Drinnenberg I, Kelso J, Wu J, Paabo S, Zeng R . Comparison of protein and mRNA expression evolution in humans and chimpanzees. PLoS One. 2007; 2(2):e216. PMC: 1789144. DOI: 10.1371/journal.pone.0000216. View

13.

Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y . fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res. 2006; 35(Database issue):D145-8. PMC: 1669753. DOI: 10.1093/nar/gkl837. View

14.

Safran M, Chalifa-Caspi V, Shmueli O, Olender T, Lapidot M, Rosen N . Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Res. 2003; 31(1):142-6. PMC: 165497. DOI: 10.1093/nar/gkg050. View

15.

Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M . GeneCards Version 3: the human gene integrator. Database (Oxford). 2010; 2010:baq020. PMC: 2938269. DOI: 10.1093/database/baq020. View

16.

Su A, Wiltshire T, Batalov S, Lapp H, Ching K, Block D . A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004; 101(16):6062-7. PMC: 395923. DOI: 10.1073/pnas.0400782101. View

17.

Ropers H, Hamel B . X-linked mental retardation. Nat Rev Genet. 2005; 6(1):46-57. DOI: 10.1038/nrg1501. View

18.

Liu C, Bai B, Skogerbo G, Cai L, Deng W, Zhang Y . NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res. 2004; 33(Database issue):D112-5. PMC: 539995. DOI: 10.1093/nar/gki041. View

19.

Kari G, Rodeck U, Dicker A . Zebrafish: an emerging model system for human disease and drug discovery. Clin Pharmacol Ther. 2007; 82(1):70-80. DOI: 10.1038/sj.clpt.6100223. View

20.

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View