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GeneCards Version 3: the human gene integrator

M. Safran, I. Dalah, J. Alexander, N. Rosen, T. Iny Stein, M. Shmoish, N. Nativ, I. Bahir, T. Doniger, H. Krug, A. Sirota-Madi, T. Olender (+4 others)
2010 Database: The Journal of Biological Databases and Curation  
Its gene-centric content is automatically mined and integrated from over 80 digital sources, resulting in a web-based deep-linked card for each of >73 000 human gene entries, encompassing the following  ...  We now introduce GeneCards Version 3, featuring a speedy and sophisticated search engine and a revamped, technologically enabling infrastructure, catering to the expanding needs of biomedical researchers  ...  Version 3, David Warshawsky for providing the model and data sources for highly-targeted reagents, Edna Ben-Asher and Orit Shmueli for defining the initial SNP filtering algorithms, Ido Zak for improving  ... 
doi:10.1093/database/baq020 pmid:20689021 pmcid:PMC2938269 fatcat:sgouahhtubhvxo7qkzn2qugaqu

VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases

Chien-Yueh Lee, Amrita Chattopadhyay, Li-Mei Chiang, Jyh-Ming Jimmy Juang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y Chuang
2019 Database: The Journal of Biological Databases and Curation  
species: human, mouse and zebrafish.  ...  Integrated analysis of DNA variants and gene expression profiles may facilitate precise identification of gene regulatory networks involved in disease mechanisms.  ...  Acknowledgement We thank Melissa Stauffer, PhD, for editing the manuscript. Conflict of interest. None declared.  ... 
doi:10.1093/database/baz075 pmid:31317185 pmcid:PMC6637258 fatcat:2of45eilerbo7eopjw227vyq6m

A one-step source for information about human genes

Melanie Nelson
2000 Genome Biology  
The GeneCards website provides a convenient and integrated interface to a variety of information about human genes. Content  ...  The site is updated via versioned releases. The most recent release is version 2.16, dated 13 July 2000.  ...  Wish list It would be useful to be able to follow a link from each GeneCard to a listing of related genes also covered by the site.  ... 
doi:10.1186/gb-2000-1-3-reports2049 fatcat:poxf5miesbfbjlvbfiq2eclqku

Non-redundant compendium of human ncRNA genes in GeneCards

Frida Belinky, Iris Bahir, Gil Stelzer, Shahar Zimmerman, Naomi Rosen, Noam Nativ, Irina Dalah, Tsippi Iny Stein, Noa Rappaport, Toutai Mituyama, Marilyn Safran, Doron Lancet
2012 Computer applications in the biosciences : CABIOS  
California (USA); the Crown Human Genome Center at the Weizmann Institute of Science and the SysKid-EU FP7 project number (241544). Conflict of Interest: None declared.  ...  We have strived to generate a comprehensive integrated list of human ncRNA genes within GeneCards, thereby placing them in the context of a complete human gene compendium.  ...  GeneCards is an integrated human gene compendium, which strives to consolidate information about all human genes (Safran et al., 2010; Stelzer et al., 2011) .  ... 
doi:10.1093/bioinformatics/bts676 pmid:23172862 fatcat:eva7zsn2bbg3zfevzxohslvdxu

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

M. Safran, I. Solomon, O. Shmueli, M. Lapidot, S. Shen-Orr, A. Adato, U. Ben-Dor, N. Esterman, N. Rosen, I. Peter, T. Olender, V. Chalifa-Caspi (+1 others)
2002 Bioinformatics  
Motivation: In the post-genomic era, functional analysis of genes requires a sophisticated interdisciplinary arsenal.  ...  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  ...  ACKNOWLEDGMENTS This work was supported by the Weizmann Institute Crown Human Genome Center and by DoubleTwist Inc.  ... 
doi:10.1093/bioinformatics/18.11.1542 pmid:12424129 fatcat:n47iqtcmezbfzczxibfubq5hye

In-silico human genomics with GeneCards

Gil Stelzer, Irina Dalah, Tsippi Stein, Yigeal Satanower, Naomi Rosen, Noam Nativ, Danit Oz-Levi, Tsviya Olender, Frida Belinky, Iris Bahir, Hagit Krug, Paul Perco (+4 others)
2011 Human Genomics  
Since 1998, the bioinformatics, systems biology, genomics and medical communities have enjoyed a synergistic relationship with the GeneCards database of human genes (  ...  This human gene compendium was created to help to introduce order into the increasing chaos of information flow.  ...  Figure 3 . 3 Protein expression profile of the KRT1 gene for normal human tissues, cell lines and body fluids. Figure 2 . 2 SysKid data pipeline.  ... 
doi:10.1186/1479-7364-5-6-709 pmid:22155609 pmcid:PMC3525253 fatcat:szb36ui2mnbyzoup6jvadonurm

GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases

M. Shklar
2004 Nucleic Acids Research  
This work was funded by the Weizmann Institute Crown Human Genome Center and the Abraham and Judith Goldwasser Foundation, and by XenneX Inc.  ...  ACKNOWLEDGEMENTS The authors wish to thank Ron Ophir, Itai Yanai, Tsippi Iny Stein and the reviewer for their important suggestions and help.  ...  INTRODUCTION GeneCards ( (1) is an automated, integrated database of human genes, proteins and associated phenotypes, which strives to provide a comprehensive and  ... 
doi:10.1093/nar/gki122 pmid:15608261 pmcid:PMC540076 fatcat:nsxin72ru5efxhn3u325tojx7a

GeneCards: integrating information about genes, proteins and diseases

M Rebhan
1997 Trends in Genetics  
This resource integrates information extracted from 'lower level databases' dealing with human genes, the functions of the proteins they encode, and the diseases in which they are involved.  ...  The GeneCard provides the following information: (1) the official gone name as approved by the HUGO/GDB nomenclature committee3; (2) a list of synonyms; (3) homologous genes in the mouse; (4) the chromosomal  ... 
doi:10.1016/s0168-9525(97)01103-7 pmid:9097728 fatcat:2k5nep2tcfff5lwryyqx4mhmsq

Rational confederation of genes and diseases: NGS interpretation via GeneCards, MalaCards and VarElect

Noa Rappaport, Simon Fishilevich, Ron Nudel, Michal Twik, Frida Belinky, Inbar Plaschkes, Tsippi Iny Stein, Dana Cohen, Danit Oz-Levi, Marilyn Safran, Doron Lancet
2017 BioMedical Engineering OnLine  
The GeneCards suite databases, which include GeneCards (human genes), MalaCards (human diseases) and PathCards (human pathways) together with additional tools, are presented with the focus on MalaCards  ...  A key challenge in the realm of human disease research is next generation sequencing (NGS) interpretation, whereby identified filtered variant-harboring genes are associated with a patient's disease phenotypes  ...  Acknowledgements The authors thank C. Paul Morrey, Moran Gershoni, and the W.I.S. GeneCards and LifeMap Sciences teams for fruitful collaborations and comments.  ... 
doi:10.1186/s12938-017-0359-2 pmid:28830434 pmcid:PMC5568599 fatcat:nr5iblpqh5bn5glqnrgelrdehm

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

M. Safran
2003 Nucleic Acids Research  
ACKNOWLEDGEMENTS The work described in this paper was supported by the Weizmann Institute of Sciences Crown Human Genome Center and by the Abraham and Judith Goldwasser foundation.  ...  INTRODUCTION Since 1997, GeneCards TM (1-3) cards/, an automated, integrated database of human genes, genomic maps, proteins, and diseases, with software that retrieves,  ...  Figure 2 shows an extract of GeneCards GeneLoc results incorporated into UDB, integrating GeneCards numbers and gene positions with the markers and contigs that are already present in the database.  ... 
doi:10.1093/nar/gkg050 pmid:12519968 pmcid:PMC165497 fatcat:l4k544txibb7xhqlg2fhte7er4

GeneAnnot: Interfacing GeneCards with high-throughput gene expression compendia

V. Chalifa-Caspi
2003 Briefings in Bioinformatics  
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.  ...  The interpretation of microarray expression results often includes extensive efforts to identify and annotate the gene representatives immobilised on the arrays.  ...  Acknowledgments This work was supported by grants from the Abraham and Judy Goldwasser Fund and from the Crown Human Genome Center.  ... 
doi:10.1093/bib/4.4.349 pmid:14725348 fatcat:fttqkhkh6zeydgiya5jceqnkjq

Genic insights from integrated human proteomics in GeneCards

Simon Fishilevich, Shahar Zimmerman, Asher Kohn, Tsippi Iny Stein, Tsviya Olender, Eugene Kolker, Marilyn Safran, Doron Lancet
2016 Database: The Journal of Biological Databases and Curation  
GeneCards is a one-stop shop for searchable human gene annotations  ...  GeneCards, the human gene compendium, is a genecentric database integrating data for 152 704 human genes from 125 sources (11) .  ...  Methods Mining and integrating human proteomes Protein expression sources provided data either via txt files (PaxDb version 3.0 integrated datasets, MOPED version 2.5, MaxQB 09/2013) or via API methods  ... 
doi:10.1093/database/baw030 pmid:27048349 pmcid:PMC4820835 fatcat:o2qmsm6l2ve7bpyvhbj2pnu6re

GIFtS: annotation landscape analysis with GeneCards

Arye Harel, Aron Inger, Gil Stelzer, Liora Strichman-Almashanu, Irina Dalah, Marilyn Safran, Doron Lancet
2009 BMC Bioinformatics  
The GIFtS tool, linked from the GeneCards home page, facilitates browsing the human genome by searching for the annotation level of a specified gene, retrieving a list of genes within a specified range  ...  GeneCards ® is a gene-centric compendium of rich annotative information for over 50,000 human gene entries, building upon 68 data sources, including Gene Ontology (GO), pathways, interactions, phenotypes  ...  GeneALaCart), Justin Alexander (currently working on the assimilation of GIFtS in GeneCards Version 3), Emily Brewster (Quality Assurance), and the reviewers.  ... 
doi:10.1186/1471-2105-10-348 pmid:19852797 pmcid:PMC2774327 fatcat:e7jfqzhntrfpnongo5zgulj72m

GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support

M. Rebhan, V. Chalifa-Caspi, J. Prilusky, D. Lancet
1998 Bioinformatics  
Analyses of the interactions of users with the Web interface of GeneCards triggered development of easy-to-scan displays optimized for human browsing.  ...  It is a freely accessible Web resource that offers one hypertext 'card' for each of the more than 7000 human genes that currently have an approved gene symbol published by the HUGO/GDB nomenclature committee  ...  Acknowledgements This work has been supported by a fellowship from the Minerva Stiftung fuer die Forschung (to M.R.), the Israel Academy of Science, the Israeli Ministry of Science, the Henri and  ... 
doi:10.1093/bioinformatics/14.8.656 pmid:9789091 fatcat:w4rmc4ew6rg3jnn4hcvuih6xxe

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

Simon Fishilevich, Ron Nudel, Noa Rappaport, Rotem Hadar, Inbar Plaschkes, Tsippi Iny Stein, Naomi Rosen, Asher Kohn, Michal Twik, Marilyn Safran, Doron Lancet, Dana Cohen
2017 Database: The Journal of Biological Databases and Curation  
We present GeneHancer, a novel database of human enhancers and their inferred target genes, in the framework of GeneCards.  ...  GeneHancer: genome-wide integration of enhancers and target genes in GeneCards.  ...  (Massachusetts, USA); Crown Human Genome Center at the Weizmann Institute of Science.  ... 
doi:10.1093/database/bax028 pmid:28605766 pmcid:PMC5467550 fatcat:xslg453wargdbalhgq7rmj73pq
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