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The DifferentialNet database of differential protein–protein interactions in human tissues

Omer Basha, Rotem Shpringer, Chanan M Argov, Esti Yeger-Lotem
2017 Nucleic Acids Research  
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

Yinuo Wang, Songbiao Zhu, Chengcheng Liu, Haiteng Deng, Zhenyu Zhang, A.Seval Ozgu-Erdinc
2021 BioMed Research International  
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

Rakibul Islam, Liton Ahmed, Bikash Kumar Paul, Kawsar Ahmed, Touhid Bhuiyan, Mohammad Ali Moni
2021 Journal of Genetic Engineering and Biotechnology  
The DifferentialNet database was used to construct Proteinprotein 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

Fen Ma, Siwei Zhang, Lianhao Song, Bozhi Wang, Lanlan Wei, Fengmin Zhang
2021 Cell & Bioscience  
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

La Cognata, Gentile, Aronica, Cavallaro
2020 Cells  
roles based on proteinprotein 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]

Omer Basha, Chanan Argov, Raviv Artzy, Yazeed Zoabi, Idan Hekselman, Liad Alfandari, Vered Chalifa-Caspi, Esti Yeger-Lotem
2019 bioRxiv   pre-print
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

Jose A. Santiago, Virginie Bottero, Judith A. Potashkin
2020 International Journal of Molecular Sciences  
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

Jaana van Gastel, Hanne Leysen, Paula Santos-Otte, Jhana O. Hendrickx, Abdelkrim Azmi, Bronwen Martin, Stuart Maudsley
2019 Aging  
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

Jinzhong Zhang, Xiuzhi Zhang, Lingxiao Wang, Chunyan Kang, Ningning Li, Zhefeng Xiao, Liping Dai
2021 PeerJ  
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

Yabo Ouyang, Jiming Yin, Wenjing Wang, Hongbo Shi, Ying Shi, Bin Xu, Luxin Qiao, Yingmei Feng, Lijun Pang, Feili Wei, Xianghua Guo, Ronghua Jin (+1 others)
2020 Clinical Infectious Diseases  
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

Jose A. Santiago, Virginie Bottero, Judith A. Potashkin
2019 Frontiers in Neuroscience  
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]

Rahul Pande, Yinyin Huang, Erin Teeple, Pooja Joshi, Amilcar Flores-Morales, Martine Latta- Mahieu, S. Pablo Sardi, Angel Cedazo-Minguez, Katherine W. Klinger, Stephen L. Madden, Deepak Rajpal, Dinesh Kumar
2021 bioRxiv   pre-print
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

Pandiyan Muthuramalingam, Rajendran Jeyasri, Alaguvel Valliammai, Anthonymuthu Selvaraj, Chandrasekar Karthika, Shanmugaraj Gowrishankar, Shunmugiah Karutha Pandian, Manikandan Ramesh, Jen-Tsung Chen
2020 Genomics  
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

Guangyan Zhou, Othman Soufan, Jessica Ewald, Robert E W Hancock, Niladri Basu, Jianguo Xia
2019 Nucleic Acids Research  
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

Yinlan Liu, Yuhan Yang, Yan Luo, Juan Wang, Xiangyun Lu, Zongxing Yang, Jin Yang
2020 Aging  
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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