Gene ORGANizer: linking genes to the organs they affect

Gokhman, David; Kelman, G. R.; Amartely, Adir; Gershon, Guy; Tsur, Shira; Carmel, Liran

doi:10.1093/nar/gkx302

Cited by 47 publications

(51 citation statements)

References 47 publications

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“…e. Significant enrichments of human disease phenotypes for genes assigned to novel craniofacial enhancer segments as reported by GREAT 58 . f. Enrichment of anatomical expression of transcription factors identified as potentially regulated by novel craniofacial enhancer segments as reported by GeneORGANizer 88 . Heat indicates fold enrichment of expression in individual anatomical region or organ.…”

Section: Resultsmentioning

confidence: 96%

“…These novel craniofacial enhancer segmentations were assessed for gene ontology and functional enrichments based on assigned target genes using GREAT (v3.0.0) 58 . Genes identified as transcriptional regulators by GREAT were assessed for enrichment of anatomical expression using default parameters in GeneORGANizer 88 . Sequence from novel craniofacial enhancer segmentations was extracted from hg19 using fastaFromBed within BEDTools 84 .…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

High Resolution Epigenomic Atlas of Early Human Craniofacial Development

Wilderman

Kron²,

VanOudenhove³

et al. 2017

Preprint

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12 13 Defects in embryonic patterning resulting in craniofacial abnormalities are common birth 14 defects affecting up to 1 in 500 live births worldwide, and are mostly non-syndromic. 15 The regulatory programs that build and shape the craniofacial complex are thought to 16 be controlled by information encoded in the genome between genes and within intronic 17 sequences. Early stages of human craniofacial development have not been interrogated 18 with modern functional genomics techniques, preventing systematic analysis of genetic 19 associations with craniofacial-specific regulatory sequences. Here we describe a 20 comprehensive resource of craniofacial epigenomic annotations and systematic, 21 integrative analysis with a variety of human tissues and cell types. We identified 22 thousands of novel craniofacial enhancers and provide easily accessible genome 23 annotations for craniofacial researchers and clinicians. We demonstrate the utility of our 24 data to find likely causal variants for craniofacial abnormalities and identify a large 25 enhancer cluster that interacts with HOXA genes during craniofacial development.

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Section: Resultsmentioning

confidence: 96%

Section: Methodsmentioning

confidence: 99%

High Resolution Epigenomic Atlas of Early Human Craniofacial Development

Wilderman

Kron²,

VanOudenhove³

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…Gene ORGANizer [41] was employed to perform the target-system location analysis. DAVID Bioinformatics Resources 6.8 [42] was applied to perform GO analysis for the hub targets.…”

Section: Distribution Analysis Of Targets In Tissues/system and Gene mentioning

confidence: 99%

A Novel Combination of Vitamin C, Curcumin and Glycyrrhizic Acid Potentially Regulates Immune and Inflammatory Response Associated with Coronavirus Infections: A Perspective from System Biology Analysis

Chen¹,

Hu²,

Hood

et al. 2020

Nutrients

116

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Novel coronaviruses (CoV) have emerged periodically around the world in recent years. The recurrent spreading of CoVs imposes an ongoing threat to global health and the economy. Since no specific therapy for these CoVs is available, any beneficial approach (including nutritional and dietary approach) is worth investigation. Based on recent advances in nutrients and phytonutrients research, a novel combination of vitamin C, curcumin and glycyrrhizic acid (VCG Plus) was developed that has potential against CoV infection. System biology tools were applied to explore the potential of VCG Plus in modulating targets and pathways relevant to immune and inflammation responses. Gene target acquisition, gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment were conducted consecutively along with network analysis. The results show that VCG Plus can act on 88 hub targets which are closely connected and associated with immune and inflammatory responses. Specifically, VCG Plus has the potential to regulate innate immune response by acting on NOD-like and Toll-like signaling pathways to promote interferons production, activate and balance T-cells, and regulate the inflammatory response by inhibiting PI3K/AKT, NF-κB and MAPK signaling pathways. All these biological processes and pathways have been well documented in CoV infections studies. Therefore, our findings suggest that VCG Plus may be helpful in regulating immune response to combat CoV infections and inhibit excessive inflammatory responses to prevent the onset of cytokine storm. However, further in vitro and in vivo experiments are warranted to validate the current findings with system biology tools. Our current approach provides a new strategy in predicting formulation rationale when developing new dietary supplements.

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“…To construct a disease association map of STN, we obtained the disease-gene association data from the ORGANizer database [12]. 184 lung diseases, 1957 genes, and 6039 disease-gene pairs were considered for further analysis (see Methods) (supplementary table 2).…”

Section: Disease-gene and Disease -Disease Associations Map In Lungsmentioning

confidence: 99%

“…The disease-gene association data in the lungs or effecting lungs were retrieved from the Gene ORGANizer (geneorganizer.huji.ac.il) [12]. Gene ORGANizer is a phenotype-based curated database that links human genes to the body parts they affect.…”

Section: Construction Of Lung-specific Disease-gene and Disease-diseamentioning

confidence: 99%

Lung Disease Network Reveals the Impact of Comorbidity on SARS-CoV-2 infection

Das

2020

Preprint

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Higher mortality of COVID19 patients with comorbidity is the formidable challenge faced by the health care system. In response to the present crisis, understanding the molecular basis of comorbidity is essential to accelerate the development of potential drugs. To address this, we have measured the genetic association between COVID19 and various lung disorders and observed a remarkable resemblance. 141 lung disorders directly or indirectly linked to COVID19 result in a high-density disease-disease association network that shows a small-world property. The clustering of many lung diseases with COVID19 demonstrates a greater complexity and severity of SARS-CoV-2 infection. Furthermore, our results show that the functional protein-protein interaction modules involved RNA and protein metabolism, substantially hijacked by SARS-CoV-2, are connected to several lung disorders. Therefore we recommend targeting the components of these modules to inhibit the viral growth and improve the clinical conditions in comorbidity.

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Gene ORGANizer: linking genes to the organs they affect

Cited by 47 publications

References 47 publications

High Resolution Epigenomic Atlas of Early Human Craniofacial Development

High Resolution Epigenomic Atlas of Early Human Craniofacial Development

A Novel Combination of Vitamin C, Curcumin and Glycyrrhizic Acid Potentially Regulates Immune and Inflammatory Response Associated with Coronavirus Infections: A Perspective from System Biology Analysis

Lung Disease Network Reveals the Impact of Comorbidity on SARS-CoV-2 infection

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