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MalaCards: A Comprehensive Automatically-Mined Database of Human Diseases
2014
Current Protocols in Bioinformatics
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Systems medicine provides insights into mechanisms of human diseases, and expedites the development of better diagnostics and drugs. To facilitate such strategies, we initiated MalaCards, a compendium of human diseases and their annotations, integrating and often remodeling information from 64 data sources. MalaCards employs, among others, the proven automatic data-mining strategies established in the construction of GeneCards, our widely used compendium of human genes. The development of
doi:10.1002/0471250953.bi0124s47
pmid:25199789
fatcat:vowmssjxt5c5pnc56rviyj4ot4
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... rds poses many algorithmic challenges, such as disease name unification, integrated classification, gene-disease association, and disease-targeted expression analysis. MalaCards displays a Web card for each of >19,000 human diseases, with 17 sections, including textual summaries, related diseases, related genes, genetic variations and tests, and relevant publications. Also included are a powerful search engine and a variety of categorized disease lists. This unit describes two basic protocols to search and browse MalaCards effectively.
MOESM2 of Genome analysis and knowledge-driven variant interpretation with TGex
2019
Figshare
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Additional file 2. TGex report for the trichohepatoenteric syndrome Demo example
doi:10.6084/m9.figshare.11480619
fatcat:3hgdptj3rbgxldp5sb354ma7m4
MalaCards: an integrated compendium for diseases and their annotation
2013
Database: The Journal of Biological Databases and Curation
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Citation details: Rappaport,N., Nativ,N., Stelzer,G., et al. MalaCards: an integrated compendium for diseases and their annotation.
doi:10.1093/database/bat018
pmid:23584832
pmcid:PMC3625956
fatcat:ju462m3cezgqtkai2jjrdvatuq
Genome analysis and knowledge-driven variant interpretation with TGex
2019
BMC Medical Genomics
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The clinical genetics revolution ushers in great opportunities, accompanied by significant challenges. The fundamental mission in clinical genetics is to analyze genomes, and to identify the most relevant genetic variations underlying a patient's phenotypes and symptoms. The adoption of Whole Genome Sequencing requires novel capacities for interpretation of non-coding variants. We present TGex, the Translational Genomics expert, a novel genome variation analysis and interpretation platform,
doi:10.1186/s12920-019-0647-8
pmid:31888639
pmcid:PMC6937949
fatcat:ixi7j3mqqzflrgzaj5wwwb3xjm
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... remarkable exome analysis capacities and a pioneering approach of non-coding variants interpretation. TGex's main strength is combining state-of-the-art variant filtering with knowledge-driven analysis made possible by VarElect, our highly effective gene-phenotype interpretation tool. VarElect leverages the widely used GeneCards knowledgebase, which integrates information from > 150 automatically-mined data sources. Access to such a comprehensive data compendium also facilitates TGex's broad variant annotation, supporting evidence exploration, and decision making. TGex has an interactive, user-friendly, and easy adaptive interface, ACMG compliance, and an automated reporting system. Beyond comprehensive whole exome sequence capabilities, TGex encompasses innovative non-coding variants interpretation, towards the goal of maximal exploitation of whole genome sequence analyses in the clinical genetics practice. This is enabled by GeneCards' recently developed GeneHancer, a novel integrative and fully annotated database of human enhancers and promoters. Examining use-cases from a variety of TGex users world-wide, we demonstrate its high diagnostic yields (42% for single exome and 50% for trios in 1500 rare genetic disease cases) and critical actionable genetic findings. The platform's support for integration with EHR and LIMS through dedicated APIs facilitates automated retrieval of patient data for TGex's customizable reporting engine, establishing a rapid and cost-effective workflow for an entire range of clinical genetic testing, including rare disorders, cancer predisposition, tumor biopsies and health screening. TGex is an innovative tool for the annotation, analysis and prioritization of coding and non-coding genomic variants. It provides access to an extensive knowledgebase of genomic annotations, with intuitive and flexible configuration options, allows quick adaptation, and addresses various workflow requirements. It thus simplifies and accelerates variant interpretation in clinical genetics workflows, with remarkable diagnostic yield, as exemplified in the described use cases. TGex is available at http://tgex.genecards.org/.
Rational confederation of genes and diseases: NGS interpretation via GeneCards, MalaCards and VarElect
2017
BioMedical Engineering OnLine
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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. This necessitates bioinformatics tools linked to comprehensive knowledgebases. 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 utility
doi:10.1186/s12938-017-0359-2
pmid:28830434
pmcid:PMC5568599
fatcat:nr5iblpqh5bn5glqnrgelrdehm
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... for NGS interpretation as well as for large scale bioinformatic analyses.
MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search
2016
Nucleic Acids Research
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The MalaCards human disease database (http://www. malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of ∼20 000 disease entries, in six global categories. It portrays a broad array of annotation topics in 15 sections, including Summaries, Symptoms, Anatomical Context, Drugs, Genetic Tests, Variations and Publications. The Aliases and Classifications section reflects an algorithm for disease name integration across
doi:10.1093/nar/gkw1012
pmid:27899610
pmcid:PMC5210521
fatcat:gc65doqdurcxrdfs4fbqhanxbi
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... -conflicting sources, providing effective annotation consolidation. A central feature is a balanced Genes section, with scores reflecting the strength of disease-gene associations. This is accompanied by other gene-related disease information such as pathways, mouse phenotypes and GO-terms, stemming from MalaCards' affiliation with the GeneCards Suite of databases. MalaCards' capacity to inter-link information from complementary sources, along with its elaborate search function, relational database infrastructure and convenient data dumps, allows it to tackle its rich disease annotation landscape, and facilitates systems analyses and genome sequence interpretation. MalaCards adopts a 'flat' disease-card approach, but each card is mapped to popular hierarchical ontologies (e.g. International Classification of Diseases, Human Phenotype Ontology and Unified Medical Language System) and also contains information about multi-level relations among diseases, thereby providing an optimal tool for disease representation and scrutiny.
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards
2017
Database: The Journal of Biological Databases and Curation
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These authors contributed equally to this work. Citation details: Fishilevich,S., Nudel,R., Rappaport,N. et al. GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. Abstract 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
doi:10.1093/database/bax028
pmid:28605766
pmcid:PMC5467550
fatcat:xslg453wargdbalhgq7rmj73pq
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... l 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. Employing an integration algorithm that aims to remove redundancy, GeneHancer portrays 285 000 integrated candidate enhancers (covering 12.4% of the genome), 94 000 of which are derived from more than one source, and each assigned an annotation-derived confidence score. GeneHancer subsequently links enhancers to genes, using: tissue co-expression correlation between genes and enhancer RNAs, as well as enhancer-targeted transcription factor genes; expression quantitative trait loci for variants within enhancers; and capture Hi-C, a promoter-specific genome conformation assay. The individual scores based on each of these four methods, along with gene-enhancer genomic distances, form the basis for GeneHancer's combinatorial likelihood-based scores for enhancer-gene pairing. Finally, we define 'elite' enhancergene relations reflecting both a high-likelihood enhancer definition and a strong enhancer-gene association. GeneHancer predictions are fully integrated in the widely used GeneCards Suite, whereby candidate enhancers and their annotations are displayed on every relevant GeneCard. This assists in the mapping of non-coding variants to enhancers, and via the linked genes, forms a basis for variant-phenotype interpretation of whole-genome sequences in health and disease.
ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions
2016
Database: The Journal of Biological Databases and Curation
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Citation details: Marenco,L., Wang,R., McDougal,R. et al. ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. Abstract We present here an exploration of the evolution of three well-established, web-based resources dedicated to the dissemination of information related to olfactory receptors (ORs) and their functional ligands, odorants. These resources are: the Olfactory Receptor Database (ORDB), the Human Olfactory Data Explorer (HORDE) and
doi:10.1093/database/baw132
pmid:27694208
pmcid:PMC5045865
fatcat:es3j5ulb4resbhbyg6z4b5s7qi
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... Ractor. ORDB is a repository of genomic and proteomic information related to ORs and other chemosensory receptors, such as taste and pheromone receptors. Three companion databases closely integrated with ORDB are OdorDB, ORModelDB and OdorMapDB; these resources are part of the SenseLab suite of databases (http://senselab.med.yale.edu). HORDE (http://genome.weizmann.ac.il/horde/) is a semi-automatically populated database of the OR repertoires of human and several mammals. ODORactor (http://mdl.shsmu.edu.cn/ ODORactor/) provides information related to OR-odorant interactions from the perspective of the odorant. All three resources are connected to each other via web-links.
VarElect: the phenotype-based variation prioritizer of the GeneCards Suite
2016
BMC Genomics
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Next generation sequencing (NGS) provides a key technology for deciphering the genetic underpinnings of human diseases. Typical NGS analyses of a patient depict tens of thousands non-reference coding variants, but only one or very few are expected to be significant for the relevant disorder. In a filtering stage, one employs family segregation, rarity in the population, predicted protein impact and evolutionary conservation as a means for shortening the variation list. However, narrowing down
doi:10.1186/s12864-016-2722-2
pmid:27357693
pmcid:PMC4928145
fatcat:zbmio3et65h23phhmmgyve46z4
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... rther towards culprit disease genes usually entails laborious seeking of gene-phenotype relationships, consulting numerous separate databases. Thus, a major challenge is to transition from the few hundred shortlisted genes to the most viable disease-causing candidates.
Distinct Expression/Function of Potassium and Chloride Channels Contributes to the Diverse Volume Regulation in Cortical Astrocytes of GFAP/EGFP Mice
2012
PLoS ONE
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The PCR data revealed the existence of two astrocytic subpopulations markedly differing in their gene expression levels for inwardly rectifying K + channels (Kir4.1), K 2P channels (TREK-1 and TWIK-1) ...
Barium chloride (1 mM), which was shown to block the inwardly rectifying K + channel TWIK-1 [27] , markedly reduced the swelling of HR-astrocytes, thus suggesting that TWIK-1 channels contribute to K ...
On the other hand, HR-astrocytes strongly express TWIK-1, which is responsible for enhanced K + uptake and their swelling. ...
doi:10.1371/journal.pone.0029725
pmid:22253765
pmcid:PMC3256164
fatcat:prfoqkft6ffo7dvf6mm7wrcm2q
Potassium Channel in the Mitochondria of Human Keratinocytes
2014
Journal of Investigative Dermatology
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Immunofluorescent methods and western blotting have suggested the possibility of the presence of TASK-1, 2 and 3 (tandem pore domain acidsensitive K þ channels), TREK-1 (TWIK-related K þ channel) and 2 ...
, and TRAAK (TWIK-related arachidonic acid-stimulated K þ channel) channels in plasma membrane of these cells and the TASK-3 channel in the mitochondria of keratinocytes (Kang et al., 2007; Rusznak et ...
doi:10.1038/jid.2013.422
pmid:24126847
fatcat:7jddvyj5bve5rle2ijndqxi3me
Molecular factors in migraine
2016
OncoTarget
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the insertion/deletion polymorphism Abbreviations: MA -migraine with aura; MO -migraine without aura; MTHFR -methylenetetrahydrofolate reductase; KCNK18 -potassium channel subfamily K member 18; TRESK -TWIK-related ...
doi:10.18632/oncotarget.9367
pmid:27191890
pmcid:PMC5226615
fatcat:sku63h6sv5c2xkosuyn4je756e
Non-redundant compendium of human ncRNA genes in GeneCards
2012
Computer applications in the biosciences : CABIOS
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ACKNOWLEDGEMENTS We thank Michal Twik for helpful discussions. Funding: LifeMap Sciences Inc. ...
doi:10.1093/bioinformatics/bts676
pmid:23172862
fatcat:eva7zsn2bbg3zfevzxohslvdxu
Mitochondrialne kanały potasowe: podsumowanie
2018
Postepy biochemii
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Up to now, only one member of this family, TWIK-Related Acid-Sensitive K + Channel 3 (TASK-3), has been shown to reside in mitochondria [15] [16] [17] [18] [19] . ...
dependent potassium channels; mitoSK Ca -mitochondrial small--conductance K Ca channel; OMM -outer mitochondrial membrane, PAX -paxilline; ROMK2 -renal outer medullary K + channel (Kir1.1b); TASK-3 -TWIK-related ...
doi:10.18388/pb.2018_132
fatcat:urqjl2u4srhf5pcowl4x3zqq3i
Altered Astrocytic Swelling in the Cortex of α-Syntrophin-Negative GFAP/EGFP Mice
2014
PLoS ONE
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channels ClC1 and ClC2; Glul encodes glutamine synthetase (GS); Trpv4 encodes transient receptor potential vanilloid 4 channels TRPV4; Kcnk1, Kcnk2, Kcnk9 and Kcnk10 code two pore domain K + channels TWIK ...
channels ClC1 and ClC2; Glul encodes glutamine synthetase; Trpv4 encodes the transient receptor potential vanilloid 4 channel TRPV4; Kcnk1, Kcnk2, Kcnk9 and Kcnk10 code the two pore domain K + channels TWIK ...
doi:10.1371/journal.pone.0113444
pmid:25426721
pmcid:PMC4245134
fatcat:t44yogtjjzebbgdm63fd6tiskm
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