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The DifferentialNet database of differential protein–protein interactions in human tissues
2017
Nucleic Acids Research
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DifferentialNet is a novel database that provides users with differential interactome analysis of human tissues (http://netbio.bgu.ac.il/diffnet/). ...
Users query DifferentialNet by protein, and retrieve its differential protein-protein interactions (PPIs) per tissue via an interactive graphical interface. ...
Vered Chalifa-Caspi for their help in analyzing the HPA samples to obtain counts. ...
doi:10.1093/nar/gkx981
pmid:29069447
pmcid:PMC5753382
fatcat:aklf2hdc4zbfnimkiggqobvqye
Text Mining and Hub Gene Network Analysis of Endometriosis
2021
BioMed Research International
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The 15 proteins that interacted with 20 or more other proteins were identified as the hub proteins of the endometriosis-associated protein network. ...
Protein-protein interaction analysis was conducted on the genes significantly cooccurring with endometriosis to identify the endometriosis-associated hub genes. ...
This study was supported by the National Key R&D Program of China (2017YFC1001204). 9 BioMed Research International ...
doi:10.1155/2021/5517145
pmid:34917684
pmcid:PMC8670927
fatcat:6zbqfcwdobdadg3nj3mvjyieeu
Identification of molecular biomarkers and pathways of NSCLC: insights from a systems biomedicine perspective
2021
Journal of Genetic Engineering and Biotechnology
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The DifferentialNet database was used to construct Protein–protein interaction (PPI) network and visualized it with the Cytoscape software. ...
Outcomes indicate that Stratifin may play a crucial role in the development of NSCLC. ...
The authors are grateful who have participated in this research work. We thank the anonymous referees for their useful suggestions. ...
doi:10.1186/s43141-021-00134-1
pmid:33742334
fatcat:c3x25khgivc5th7ow2etemlt2m
Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level
2021
Cell & Bioscience
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Main body This study reviewed the history of ligand-receptor and presents the databases which store ligand-receptor pairs. ...
The recently applications and research tools of ligand-receptor interactions for cell communication at single cell level by using single cell RNA sequencing have been sorted out. ...
(Binding Yes The DifferentialNet database [42] No MOAD) [23] Protein-Protein Interaction Sites-Yes Unified Human Interactome data-No base (PPInS) [43] base (UniHI) [24] UniLectin3D [44] Yes Interolog ...
doi:10.1186/s13578-021-00635-z
pmid:34217372
pmcid:PMC8254218
fatcat:ox4nvuvednhndbsfb55xuepjn4
Splicing Players Are Differently Expressed in Sporadic Amyotrophic Lateral Sclerosis Molecular Clusters and Brain Regions
2020
Cells
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roles based on protein–protein interactions. ...
A substantial number of genes (184) displayed significant expression changes in tissue types or disease states, were implicated in distinct splicing complexes and showed different topological hierarchical ...
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/cells9010159
pmid:31936368
pmcid:PMC7017305
fatcat:n75yw6shsrcobcyb5nghgyur4i
Differential network analysis of human tissue interactomes highlights tissue-selective processes and genetic disorder genes
[article]
2019
bioRxiv
pre-print
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Motivation: Differential network analysis, designed to highlight interaction changes between conditions, is an important paradigm in network biology. ...
Summary: Altogether, our study demonstrates that differential network analysis of human tissue interactomes is a powerful tool for highlighting processes and genes with tissue-selective functionality and ...
INTRODUCTION Knowledge of the molecular compositions of human tissues and cells has grown immensely in recent years, owing to large-scale omics projects such as the Human Protein Atlas (Uhlen et al., ...
doi:10.1101/612143
fatcat:n3lkoiya7jbzlmsfctutm6rcrq
Transcriptomic and Network Analysis Identifies Shared and Unique Pathways across Dementia Spectrum Disorders
2020
International Journal of Molecular Sciences
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Upregulated genes in FTD were associated with ECM receptor interactions and the lysosome, whereas downregulated genes were involved in glutamatergic synapse and MAPK signaling. ...
Methods: In this study, we compared the transcriptome from the frontal cortex of patients with AD, VaD, and FTD to identify dysregulated pathways. ...
Tissue specific networks derived from the protein-protein interaction database from human frontal cortex were constructed for each disease. ...
doi:10.3390/ijms21062050
pmid:32192109
fatcat:4vwrvrv2snc5nbt6tucfgkpici
The RXFP3 receptor is functionally associated with cellular responses to oxidative stress and DNA damage
2019
Aging
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Analyzing the effects of oxidizing (H2O2) and DNA-damaging (camptothecin) stressors on the interacting partners of RXFP3 using Affinity Purification-Mass Spectrometry, we found multiple proteins linked ...
We recently showed that G protein-coupled receptor (GPCR) kinase interacting protein 2 (GIT2) plays a key role in both DNA damage and oxidative stress. ...
The proteins consistently associated with the RXFP3 receptor following exposure to hydrogen peroxide were analyzed using a human hypothalamic tissue database derived from DIFFERENTIALNET (http://netbio.bgu.ac.il ...
doi:10.18632/aging.102528
pmid:31794429
pmcid:PMC6932917
fatcat:t7nolxlnz5g2fehy34jwqnglii
Multiomics-based analyses of KPNA2 highlight its multiple potentials in hepatocellular carcinoma
2021
PeerJ
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The clinicopathological significance of KPNA2 was highlighted through the in-depth analyses at multilevels. ...
Herein multi-omic alterations of KPNA2 were analyzed at genetic, epigenetic, transcript, and protein levels with evaluation of their relevance with clinicopathological features of HCC by integrative analyses ...
JM Zeng from University of Macau and his team for their help in the bioinformatics analysis. ...
doi:10.7717/peerj.12197
pmid:34616632
pmcid:PMC8462373
fatcat:skowsucw6vgdvicz6fgujfdqf4
Down-regulated gene expression spectrum and immune responses changed during the disease progression in COVID-19 patients
2020
Clinical Infectious Diseases
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Cough and fever were the top symptoms in the 11 COVID-2019 cases. The elder age, more neutrophils numbers and higher C-reactive protein level were found in severe cases. ...
The number of DEGs increased with the disease progress, and decreased after initial treatment. ...
Protein-protein interaction (PPI) analysis of DEGs was based on tissue specific PPI data from the DifferentialNet database, and the images were examined using NetworkAnalyst platform [12] . ...
doi:10.1093/cid/ciaa462
pmid:32307550
pmcid:PMC7188184
fatcat:e72vjipe5bafjduladpgnmuwuy
Transcriptomic and Network Analysis Highlight the Association of Diabetes at Different Stages of Alzheimer's Disease
2019
Frontiers in Neuroscience
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AD and T2D were involved in the phosphatidylinositol 3-kinase and protein kinase B/Akt (PI3K-AKT) signaling pathway, a major mediator of insulin signaling in the body. ...
Furthermore, how T2D may contribute to the progression of AD is a subject of extensive investigation. ...
In NetworkAnalyst, we used the tissue-specific networks derived from the protein-protein interaction database from human whole blood. ...
doi:10.3389/fnins.2019.01273
pmid:31849586
pmcid:PMC6895844
fatcat:ssbd42lgefdcljgojrhjfk7ckq
Single Cell Atlas of Human Putamen Reveals Disease Specific Changes in Synucleinopathies: Parkinson's Disease and Multiple System Atrophy
[article]
2021
bioRxiv
pre-print
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Although both PD and MSA are manifestations of alpha-synuclein protein aggregation, we observed that both the diseases have distinct cell-type specific changes. ...
Contrary to PD microglia, we found absence of upregulated unfolded protein response in MSA microglia compared to controls. ...
[39] and DifferentialNet database [40] . ...
doi:10.1101/2021.05.06.442950
fatcat:2xxhyvajrbdg5lxds5wjcsujwa
Global multi-omics and systems pharmacological strategy unravel the multi-targeted therapeutic potential of natural bioactive molecules against COVID-19: An in silico approach
2020
Genomics
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In this study, multi-omics and systems pharmacology analyses were performed to unravel the multi-targeted mechanisms of novel bioactives to combat COVID-19. ...
Understanding the immunological behavior of COVID-19 cases at molecular level is essential for therapeutic development. ...
Acknowledgements The authors thank RUSA 2.
Appendix A. Supplementary data Supplementary data to this article can be found online at https:// doi.org/10.1016/j.ygeno.2020.08.003. ...
doi:10.1016/j.ygeno.2020.08.003
pmid:32771622
pmcid:PMC7410791
fatcat:s7hlp6cyejasfdxyroe7sov46i
NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis
2019
Nucleic Acids Research
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NetworkAnalyst was first released in 2014 to address the key need for interpreting gene expression data within the context of protein-protein interaction (PPI) networks. ...
The growing application of gene expression profiling demands powerful yet user-friendly bioinformatics tools to support systems-level data understanding. ...
Our newly added human tissue-specific PPI data comes from the DifferentialNet database (15) , covering 42 different tissues. ...
doi:10.1093/nar/gkz240
pmid:30931480
pmcid:PMC6602507
fatcat:yposn6zofjh7te4nwn4ubexahq
Prognostic potential of PRPF3 in hepatocellular carcinoma
2020
Aging
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pre-mRNA processing factor 3 (PRPF3) is an RNA binding protein in a core component of the exon junction complex. Abnormal PRPF3 expression is potentially associated with carcinogenesis. ...
However, the biological role of PRPF3 in hepatocellular carcinoma (HCC) remains to be determined. ...
All authors have read and approved the manuscript for publication.
CONFLICTS OF INTEREST The authors declare no potential conflicts of interest. ...
doi:10.18632/aging.102665
pmid:31926109
pmcid:PMC6977647
fatcat:avfxcggku5ezhog3rtfvr6r37m
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