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Human interactome resource and gene set linkage analysis for the functional interpretation of biologically meaningful gene sets

Xi Zhou, Pengcheng Chen, Qiang Wei, Xueling Shen, Xin Chen
2013 Computer applications in the biosciences : CABIOS  
Therefore, at a systems level, connections between individual genes in a molecular interaction network can be used to infer the collective functional linkages between biologically meaningful gene sets.  ...  Motivation: A molecular interaction network can be viewed as a network in which genes with related functions are connected.  ...  The inferred interactions and the experimentally reported protein interactions were integrated to create the HIR interactome, which contains 155 974 non-redundant interactions.  ... 
doi:10.1093/bioinformatics/btt353 pmid:23782618 fatcat:xljntbhzlnhnnib72yaroepqha

Rewiring of the Human Mitochondrial Interactome During Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis

Mohamed Taha Moutaoufik, Ramy Malty, Shahreen Amin, Qingzhou Zhang, Sadhna Phanse, Alla Gagarinova, Mara Zilocchi, Larissa Hoell, Zoran Minic, Maria Gagarinova, Hiroyuki Aoki, Jocelyn Stockwell (+16 others)
2019 iScience  
We also find that a heme-containing neurotrophic factor, neuron-derived neurotrophic factor [NENF], couples with Parkinson disease-related proteins to promote neurotrophic activity.  ...  Here, using mass spectrometry-based co-fractionation profiles and phosphoproteomics, we generated mitochondrial interaction maps of human pluripotent embryonal carcinoma stem cells and differentiated neuronal-like  ...  (A) Putative interacting proteins sharing phenotypic annotations (i) derived from MGI database (http://www.informatics.jax.org) of mouse orthologs compared to random set of protein interacting pairs,  ... 
doi:10.1016/j.isci.2019.08.057 pmid:31536960 pmcid:PMC6831851 fatcat:owmhktmmjzc4tkxztgymu2on2a

From Fuzziness to Precision Medicine: On the Rapidly Evolving Proteomics with Implications in Mitochondrial Connectivity to Rare Human Disease

Khaled A. Aly, Mohamed Taha Moutaoufik, Sadhna Phanse, Qingzhou Zhang, Mohan Babu
2021 iScience  
In this perspective article, we identified 21 mt proteins from public repositories that associate with RCC deficiency, MELAS, or ARSACS, engaging in a relatively small number of protein-protein interactions  ...  (PPIs), underscoring the need for advanced proteomic and interactomic platforms to uncover the complete scope of mt connectivity to RDs.  ...  Two factors play a critical role in interactome mapping: strength of interactions and the abundance of interacting proteins, both of which can impact the output based on the mapping method used.  ... 
doi:10.1016/j.isci.2020.102030 pmid:33521598 pmcid:PMC7820543 fatcat:awxqyvbttrdyvnihnqxvn2qlme

Data science in unveiling COVID-19 pathogenesis and diagnosis: evolutionary origin to drug repurposing

Jayanta Kumar Das, Giuseppe Tradigo, Pierangelo Veltri, Pietro H Guzzi, Swarup Roy
2021 Briefings in Bioinformatics  
With regard to this data science is playing a pivotal role in in silico analysis to gain insights into SARS-CoV-2 and the outbreak of COVID-19 in order to forecast, diagnose and come up with a drug to  ...  We consider various current COVID-19 data analytic domains such as phylogenetic analysis, SARS-CoV-2 genome identification, protein structure prediction, host-viral protein interactomics, clinical imaging  ...  Existing drug molecules have then been ranked by means of a proximity measure based on their ability to interact with their protein targets.  ... 
doi:10.1093/bib/bbaa420 pmid:33592108 pmcid:PMC7929414 fatcat:2vdkzlrrcfhvncx4d2jfepx4la

Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19

Sudhir Ghandikota, Mihika Sharma, Anil G. Jegga
2021 Patterns  
In this study, we developed an integrated network analysis framework that integrates transcriptional signatures from multiple model systems with protein-protein interaction data to find gene modules.  ...  To overcome this, unsupervised network analyses are used to identify clusters of genes that can be associated with distinct molecular mechanisms and outcomes for a disease.  ...  The consensus DEGs, along with the SARS-CoV-2-human virus-host interactome, are used to build an integrated network based on known protein-protein interactions (PPIs) retrieved from STRING database (v11  ... 
doi:10.1016/j.patter.2021.100247 pmid:33842903 pmcid:PMC8020120 fatcat:4rpv7j34fjccpefjujtpoihulm

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

Peter Csermely, Tamás Korcsmáros, Huba J.M. Kiss, Gábor London, Ruth Nussinov
2013 Pharmacology and Therapeutics  
The state-of-the-art use of chemical similarity, protein structure, protein-protein interaction, signaling, genetic interaction and metabolic networks in the discovery of drug targets is summarized.  ...  Network description and analysis not only give a systems-level understanding of drug action and disease complexity, but can also help to improve the efficiency of drug design.  ...  Academy of Sciences (TK) and by a residence at the Rockefeller Foundation Bellagio Center (PC).  ... 
doi:10.1016/j.pharmthera.2013.01.016 pmid:23384594 pmcid:PMC3647006 fatcat:osjkz6kpr5gzxomqlyenla2fvq

Meeting Report: EU–US Workshop on Molecular Signatures of DNA damage-induced Stress Responses☆Cortona, Italy, 26–30 September 2003

Miriam Sander, Christian Desaintes, Richard Pelroy, Wouter Ferro, Bennett Van Houten, Sally Amundson, Alan Lehmann, Leon Mullenders, Susanna-Assunta Sansone, Peter Stambrook
2004 Mutation research  
IntAct is a relatively new protein database initiative that provides a unified platform for analyzing data on protein-protein interactions.  ...  Because the current H. pylori interactome is based only on protein-protein interaction information, it was compared to a similarly derived interaction network in yeast.  ... 
doi:10.1016/j.mrfmmm.2004.02.009 pmid:15228042 fatcat:665kva7sjzfxpc4fgzvhaozkgy

Analysis, integration and applications of the human interactome [article]

Gautam Chaurasia, Humboldt-Universität Zu Berlin, Humboldt-Universität Zu Berlin
2017
One of the important conclusions of this study was that the current human interaction networks contain complementary information; hence, a database was developed, termed as Unified Human Interactome (UniHI  ...  To find the modifiers, a network-based modeling approach was implemented by integrating huntingtin-specific protein interaction network with gene expression data from HD patients in multiple steps.  ...  from the Unified Human Interactome database (UniHI) Chaurasia et al., 2009).  ... 
doi:10.18452/16635 fatcat:z227vy6lsje6jhtanzwwo5xik4

On an algorithmic definition for the components of the minimal cell [article]

Octavio Martinez, M. Humberto Reyes-Valdes
2018 bioRxiv   pre-print
We expect that this algorithmic approach will lead to the determination of the complete interactome of the minimal cell, which could then be experimentally validated.  ...  as a finite set of binary operators, and within this framework we show that cell elements that depend on their previous existence to be synthesized are those that are essential for cell survival.  ...  Acknowledgments 1031 We are grateful to Gerardo R. Argüello-Astorga, June Simpson and Therese A.  ... 
doi:10.1101/333682 fatcat:wawxiclconhmlkh23tw5wkhpya

EMBnet.journal 18 Suppl. A

EMBnet Journal
2012 EMBnet journal  
Protein Structure and Function Acknowledgments This work was supported by NFSR of Bulgaria project DVU 01/197.  ...  (ii) tools for querying and filtering in a semantic way such annotated databases; (iii) tools for semantic visualization of annotated protein interaction networks.  ...  Results CytoSevis is a Cytoscape plugin that is able to visualize protein interaction networks in a semantic similarity space.  ... 
doi:10.14806/ej.18.a.497 fatcat:2aexioifkfgfnipbo3btxqwvia

Protein-protein interactions: analysis and prediction [chapter]

D. Frishman, M. Albrecht, H. Blankenburg, P. Bork, E. D. Harrington, H. Hermjakob, L. Juhl Jensen, D. A. Juan, T. Lengauer, P. Pagel, V. Schachter, A. Valencia
2008 Modern Genome Annotation  
of UMLS (Unified Medical Language System) (Bodenreider 2004) .  ...  The yeast protein interaction database MPact (Guldener et al. 2006 ) provides access to 268 protein complexes based on careful literature annotation composed of 1237 different proteins plus over 1000  ... 
doi:10.1007/978-3-211-75123-7_17 fatcat:6as6bv5ezjgvxdmdzbhavyon6m

Network-based drug discovery by integrating systems biology and computational technologies

E. L. Leung, Z.-W. Cao, Z.-H. Jiang, H. Zhou, L. Liu
2012 Briefings in Bioinformatics  
to develop into new wave of network-based multi-target drugs.  ...  Network-based intervention has been a trend of curing systemic diseases, but it relies on regimen optimization and valid multi-target actions of the drugs.  ...  [36] performed MALDI-MS/MS analysis of an interactome map and identified a network of 21 differentiated regulated core proteins which are responsible for mediating apoptotic response to Ganoderic acid  ... 
doi:10.1093/bib/bbs043 pmid:22877768 pmcid:PMC3713711 fatcat:t3wp24cgyff6zechfsm5hagfji

A Survey of Computational Methods for Protein Function Prediction [chapter]

Amarda Shehu, Daniel Barbará, Kevin Molloy
2016 Big Data Analytics in Genomics  
neighbors in a protein-protein interaction network, from microarray data, or a combination of these different types of data.  ...  Automated protein function annotation or prediction is a prime problem for computational methods to tackle in the post-genomic era of big molecular data.  ...  online database of comprehensive Human Annotated and Predicted Protein Interactions (HAPPI) [59] , Known and Predicted Protein-Protein Interactions (STRING) [334] , and the Unified Human Interactome  ... 
doi:10.1007/978-3-319-41279-5_7 fatcat:pejwmwpoarhyjhulevmkbavocm

Using Genome-Wide Expression Profiling to Define Gene Networks Relevant to the Study of Complex Traits [chapter]

M.A. O'Brien, B.N. Costin, M.F. Miles
2012 International review of neurobiology  
However, as discussed in this chapter, the leveraging of such networks cannot occur without a thorough understanding of the technical and statistical factors influencing the derivation of genomic expression  ...  are all critical to defining fully useful gene networks for study of complex biology.  ...  ToppNet ranks candidate "training" set genes based on their protein-protein interactions with a "test" gene set in a protein-protein interaction network (Chen et al., 2009) .  ... 
doi:10.1016/b978-0-12-398323-7.00005-7 pmid:23195313 pmcid:PMC4104526 fatcat:64jwd3knrrggjh52lewopu6ocm

Artificial Intelligence Techniques for Colorectal Cancer Drug Metabolism: Ontologies and Complex Networks

Marcos Martinez-Romero, Jose M. Vazquez-Naya, Juan R. Rabunal, Salvador Pita-Fernandez, Ramiro Macenlle, Javier Castro-Alvarino, Leopoldo Lopez-Roses, Jose L. Ulla, Antonio V. Martinez-Calvo, Santiago Vazquez, Javier Pereira, Ana B. Porto-Pazos (+3 others)
2010 Current drug metabolism  
The molecular components involved in this metabolism are included in complex network such as metabolic pathways in order to describe all the molecular interactions in the colorectal cancer.  ...  This review presents the last studies regarding ontology and complex networks of the colorectal cancer drug metabolism and a basic topology characterization of the drug metabolic process subontology from  ...  One example of a semantic-based description of the microarray experiments is the MGED ontology [83] .  ... 
doi:10.2174/138920010791514289 pmid:20446907 fatcat:ogbfyx2hunhblkmou66acz2lbm
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