GeneCaRNA: A Comprehensive Gene-centric Database of Human Non-coding RNAs in the GeneCards Suite

Barshir, Ruth; Fishilevich, Simon; Iny-Stein, Tsippi; Zelig, Ofer; Mazor, Yaron; Guan-Golan, Yaron; Lancet, Doron

doi:10.1016/j.jmb.2021.166913

Cited by 62 publications

(44 citation statements)

References 33 publications

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“…After summarizing the targets of the four traditional Chinese medicines and removing the duplications, the total number of drug targets reached 593 ( Supplementary Table S1 ). We used osteoporosis as a keyword to search for related targets, and all genes with scores greater than 1 were obtained ( Piñero et al, 2020 ; Barshir et al, 2021 ). After merging the hit lists and removing duplicates, 1770 unique hits remained, which were disease targets; 121 shared interactors commonly existed in 593 drug targets and 1770 disease targets ( Shannon et al, 2003 ) ( Supplementary Table S2 ).…”

Section: Resultsmentioning

confidence: 99%

Qing`e Pill Inhibits Osteoblast Ferroptosis via ATM Serine/Threonine Kinase (ATM) and the PI3K/AKT Pathway in Primary Osteoporosis

Hao

Bei

et al. 2022

Front. Pharmacol.

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Osteoporosis (OP) is an aging-related disease that is the main etiology of fragility fracture. Qing’e Pill (QEP) is a mixture of traditional Chinese medicine (TCM) consisting of Eucommia ulmoides Oliv., Psoralea corylifolia L., Juglans regia L., and Allium sativum L. QEP has an anti-osteoporosis function, but the underlying mechanism remains unclear. In this study, online databases were employed to determine the chemical compounds of QEP and potential target genes in osteoporosis. Potential pathways associated with genes were defined by Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) databases. A compound–target–disease network was constructed. Hub genes screened through Cytoscape were intersected with the FerrDB database. The potential key genes were validated in HFOB 1.19 cells, and rat models were ovariectomized through Western blot, RT-qPCR, ELISA, HE staining, immunohistochemistry, and immunofluorescence analyses. The intersection targets of QEP and osteoporosis contained 121 proteins, whereas the target–pathway network included 156 pathways. We filtered five genes that stood out in the network analysis for experimental verification. The experiments validated that QEP exerted therapeutic effects on osteoporosis by inhibiting ferroptosis and promoting cell survival via the PI3K/AKT pathway and ATM. In conclusion, combining the application of network analysis and experimental verification may provide an efficient method to validate the molecular mechanism of QEP on osteoporosis.

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Section: Resultsmentioning

confidence: 99%

Qing`e Pill Inhibits Osteoblast Ferroptosis via ATM Serine/Threonine Kinase (ATM) and the PI3K/AKT Pathway in Primary Osteoporosis

Hao

Bei

et al. 2022

Front. Pharmacol.

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“…Its expression has only been found in brain tissue thus far [ 46 ]. This gene is important to neural differentiation, and mutations in it have been linked to autism spectrum disorder and an autosomal dominant form of cognitive dysfunction [ 47 ]. Mutations in Myt1L in chromosomal band 2p25.3 have been linked to intellectual disability, while Myt1L repetition has been linked to schizophrenia and MMD [ 48 ].…”

Section: Discussionmentioning

confidence: 99%

Effective biomarkers and therapeutic targets of nerve-immunity interaction in the treatment of depression: an integrated investigation of the miRNA-mRNA regulatory networks

Cai

Shi

et al. 2022

Aging

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Background: Major depressive disorder (MDD) is an emotional condition that interferes with sufferers’ work and daily life. Numerous studies have found that miRNAs play a significant role in the development of MDD and can be utilized as a biomarker for its diagnosis and therapy. However, there have been few studies on nerve-immunity interaction treatment for the brains of MMD patients. Methods: The work is performed on microarray data. We analyzed the differences of miRNAs (GSE58105, GSE81152, GSE152267, and GSE182194) and mRNA (GSE19738, GSE32280, GSE44593, GSE53987, and GSE98793) in MDD and healthy samples from GEO datasets. FunRich was used to predict the transcription factors and target genes of the miRNAs, and TF and GO enrichment analyses were performed. Then, by comparing the differential expression of the anticipated target genes and five mRNAs, intersecting mRNAs were discovered. The intersecting genes were submitted to GO and KEGG analyses to determine their functions. These intersecting potential genes and pathways that linked to MDD in neurological and immunological aspects have been identified for future investigation. Results: We discovered five hub genes: KCND2, MYT1L, GJA1, CHL1, and SNAP25, which were all up-regulated genes. However, in MMD, the equivalent miRNAs, hsa-miR-206 and hsa-miR-338-3p, were both down-regulated. These miRNAs can activate or inhibit the T cell receptor signal pathway, JAK-STAT and other signal pathways, govern immune-inflammatory response, neuronal remodeling, and mediate the onset and development of MMD Conclusions: The results of a thorough bioinformatics investigation of miRNAs and mRNAs in MDD showed that miR-338-3P and miR-206 might be effective biomarkers and possible therapeutic targets for the treatment of MDD via nerve-immunity interaction.

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“…The IMMPORT (Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine) ( https://www.immport.org ) database ( 11 ) was used to retrieve and collate 1,793 immune-related genes. A total of 1,566 COVID-19 related genes were acquired from Genecards (Department of Molecular Genetics, Weizmann Institute of Science) ( https://www.genecards.org/ ) ( 12 ). The RNA sequencing data of TCGA-LUAD patients was obtained from the TCGA data portal ( https://tcga-data.nci.nih.gov/tcga/ ).…”

Section: Methodsmentioning

confidence: 99%

The Potential Bioactive Components of Nine TCM Prescriptions Against COVID-19 in Lung Cancer Were Explored Based on Network Pharmacology and Molecular Docking

Xiao

et al. 2022

Front. Med.

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ObjectiveThe purpose of this study was to screen active components and molecular targets of nine prescriptions recommended by the National Health Commission (NHC) of China by network pharmacology, and to explore the potential mechanism of the core active components against COVID-19 with molecular docking.MethodsDifferentially expressed genes of lung adenocarcinoma (LUAD) screened by edgeR analysis were overlapped with immune-related genes in MMPORT and COVID-19-related genes in GeneCards. The overlapped genes were also COVID-19 immune-related genes in LUAD. TCMSP platform was used to identify active ingredients of the prescription, potential targets were identified by the UniProt database, and the cross genes with COVID-19 immune-related genes in LUAD were used to construct a Chinese Medicine-Logy-immune target network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the target genes of each prescription. Finally, the key active components were selected for molecular docking simulation with ACE2.ResultsWe obtained 15 overlapping immunization target genes from FPQXZ, HSYFZ, HSZFZ, and QFPDT, 16 overlapping immunization target genes from QYLFZ, SDYFZ, SRYFZ, and YDBFZ, and 17 overlapping immunization target genes from QYLXZ. ADRB2, FOS, HMOX1, ICAM1, IL6, JUN, NFKBIA, and STAT1 also had the highest-ranked therapeutic targets for 9 prescriptions, and their expressions were positively correlated with TME-related stromal score, immune score, and ESTIMATE score. Among 9 compounds with the highest frequency of occurrence in the 9 prescriptions, baicalein had the highest ACE2 binding affinity and can be well-combined into the active pocket of ACE2 It is stabilized by forming hydrogen bonds with ASN290 and ILE291 in ACE2 and hydrophobic interaction with PHE438, ILE291, and PRO415.ConclusionThe nine Chinese medicine prescriptions may play an anti-SARS-CoV-2 role via regulating viral transcription and immune function through multi-component, multi-target, and multi-pathway.

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GeneCaRNA: A Comprehensive Gene-centric Database of Human Non-coding RNAs in the GeneCards Suite

Cited by 62 publications

References 33 publications

Qing`e Pill Inhibits Osteoblast Ferroptosis via ATM Serine/Threonine Kinase (ATM) and the PI3K/AKT Pathway in Primary Osteoporosis

Qing`e Pill Inhibits Osteoblast Ferroptosis via ATM Serine/Threonine Kinase (ATM) and the PI3K/AKT Pathway in Primary Osteoporosis

Effective biomarkers and therapeutic targets of nerve-immunity interaction in the treatment of depression: an integrated investigation of the miRNA-mRNA regulatory networks

The Potential Bioactive Components of Nine TCM Prescriptions Against COVID-19 in Lung Cancer Were Explored Based on Network Pharmacology and Molecular Docking

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