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Potential role of lncRNA cyp2c91–protein interactions on diseases of the immune system

Prashanth Suravajhala, Lisette J. A. Kogelman, Gianluca Mazzoni, Haja N. Kadarmideen
2015 Frontiers in Genetics  
Apart from protein-protein interaction (PPI), gene network models such as Weighted Gene Co-expression Network Analysis (WGCNA) are used to functionally annotate lncRNAs in identifying their potential disease  ...  interaction network.  ...  Apart from protein-protein interaction (PPI), co-expression models such as Weighted Gene Co-expression Network Analysis (WGCNA; Xue et al., 2013) are used to functionally annotate lncRNAs in identifying  ... 
doi:10.3389/fgene.2015.00255 pmid:26284111 pmcid:PMC4516971 fatcat:evybmac6zba5pd7vblcqecbc54

Topological features of a gene co-expression network predict patterns of natural diversity in environmental response

David L. Des Marais, Rafael F. Guerrero, Jesse R. Lasky, Samuel V. Scarpino
2017 Proceedings of the Royal Society of London. Biological Sciences  
Our findings suggest that the gene-interaction topologies for both cold and drought stress response are non-random, with genes that show genetic variation in drought expression response (eGxE) being significantly  ...  more peripheral and cold response genes being significantly more central than genes which do not show GxE.  ...  Monroe provided stimulating discussion on the genetic architecture of abiotic stress response and expression GxE.  ... 
doi:10.1098/rspb.2017.0914 pmid:28615505 pmcid:PMC5474086 fatcat:m4nj5bkk7rcwbbqszywsuhhkq4

Modelling the structure of a ceRNA-theoretical, bipartite microRNA–mRNA interaction network regulating intestinal epithelial cellular pathways using R programming

J. M. Robinson, W. A. Henderson
2018 BMC Research Notes  
Results: We developed a network model to identify hypothetical co-regulatory motifs in a miRNA-mRNA interaction network related to epithelial function.  ...  Objective: We report a method using functional-molecular databases and network modelling to identify hypothetical mRNA-miRNA interaction networks regulating intestinal epithelial barrier function.  ...  Greg Gonye of Nanostring Technologies ® for providing assistance with Nanostring ® codesets and conceptual advice on network data structures.  ... 
doi:10.1186/s13104-018-3126-y pmid:29329594 pmcid:PMC5766989 fatcat:puy7dm2xwbgnflamvmun5ychim

NECorr, a Tool to Rank Gene Importance in Biological Processes using Molecular Networks and Transcriptome Data [article]

Christophe Victor Liseron-Monfils, Andrew Olson, Doreen Ware
2018 bioRxiv   pre-print
With the objective of ranking genes and their interactions in a selected condition or tissue, NECorr uses the molecular network topology as well as global gene expression analysis to find hub genes and  ...  Molecular network analysis techniques were developed to aid in understanding gene inter-regulation.  ...  It consists of ranking genes by importance within the molecular network as a function of gene co-expression across edges.  ... 
doi:10.1101/326868 fatcat:j3hfenrtsracrnysmtkv3a6kja

Complex Network Analysis of CA3 Transcriptome Reveals Pathogenic and Compensatory Pathways in Refractory Temporal Lobe Epilepsy

Silvia Yumi Bando, Filipi Nascimento Silva, Luciano da Fontoura Costa, Alexandre V. Silva, Luciana R. Pimentel-Silva, Luiz HM. Castro, Hung-Tzu Wen, Edson Amaro, Carlos Alberto Moreira-Filho, Ken Mills
2013 PLoS ONE  
central position in the network.  ...  Studying the whole set of CA3 valid transcripts we: i) obtained complete transcriptional networks (CO) for FS and NFS phenotypic groups; ii) examined how CO and DE networks are related; iii) characterized  ...  Ferreira, and Priscila Iamashita, from the Laboratory of Pediatric Genomics, Department of Pediatrics, FMUSP, for valuable technical help. Author Contributions  ... 
doi:10.1371/journal.pone.0079913 pmid:24278214 pmcid:PMC3836787 fatcat:6vvk4nipdvhvxgvpzxep63fujq

From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data

Danila Vella, Italo Zoppis, Giancarlo Mauri, Pierluigi Mauri, Dario Di Silvestre
2017 EURASIP Journal on Bioinformatics and Systems Biology  
In particular, the new idea to evaluate large-scale proteomic data by means of co-expression networks will be discussed presenting some examples of application.  ...  Based on these premises, we introduce the reader to the PPI and to the co-expression networks, including aspects of reconstruction and analysis.  ...  Acknowledgements The study was supported by the Italian CNR FLAGSHIP InterOmics 2015 project funded by MIUR and by Italian Ministry of Economy and Finance for the Project 'FaReBio di Qualita'.  ... 
doi:10.1186/s13637-017-0059-z pmid:28477207 pmcid:PMC5359264 fatcat:p5wgnl6p35eojozxictrmedm64

Modular network inference between miRNA–mRNA expression profiles using weighted co-expression network analysis

Nisar Wani, Debmalya Barh, Khalid Raza
2021 Journal of Integrative Bioinformatics  
Connecting transcriptional and post-transcriptional regulatory networks solves an important puzzle in the elucidation of gene regulatory mechanisms.  ...  We construct gene and miRNA co-expression modules using the weighted gene co-expression network analysis (WGCNA) method and establish the significance of these modules (Genes/miRNAs) for cancer phenotype  ...  We apply these important network topological measures to locate central players in the interaction network depicted in Figure 6 .  ... 
doi:10.1515/jib-2021-0029 pmid:34800012 pmcid:PMC8709739 fatcat:6h2edskldnaahctyth25q45ebe

Transcriptional Network Analysis Reveals that AT1 and AT2 Angiotensin II Receptors Are Both Involved in the Regulation of Genes Essential for Glioma Progression

Hátylas Azevedo, André Fujita, Silvia Yumi Bando, Priscila Iamashita, Carlos Alberto Moreira-Filho, Sadashiva Karnik
2014 PLoS ONE  
Moreover, other genes co-expressing with the DE genes were considered in these analyses in order to support the identification of enriched functions and pathways.  ...  Gene expression data was evaluated through transcriptional network modeling to identify how differentially expressed (DE) genes are connected to each other.  ...  We are also grateful to the University of São Paulo for providing the infrastructure to perform the experiments whose results were discussed in the manuscript.  ... 
doi:10.1371/journal.pone.0110934 pmid:25365520 pmcid:PMC4217762 fatcat:cw6lx46bybdqpl5o27k7ojvwky

Revealing gene regulation and associations through biological networks

Christophe Liseron-Monfils, Doreen Ware
2015 Current Plant Biology  
In crop species, one aim of QTL analysis is to define genetic regions responsible for architectural and stress-related phenotypes, e.g., the response to water deficit and the efficiency of nitrogen use  ...  Moreover, the outcome is not always guaranteed, as it depends upon the rate of crossing-over in the http://dx.  ...  The development of co-expression and molecular networks will be described.  ... 
doi:10.1016/j.cpb.2015.11.001 fatcat:oz6mwmi6nrgnlgmnahp7bc7yim

Dynamic modeling of transcriptional gene regulatory network uncovers distinct pathways during the onset of Arabidopsis leaf senescence

Bharat Mishra, Yali Sun, TC Howton, Nilesh Kumar, M. Shahid Mukhtar
2018 npj Systems Biology and Applications  
Network structural and functional analyses revealed important nodes within each module of these co-expression networks.  ...  Here, we constructed a computational pipeline that integrates senescence-related co-expression networks with transcription factor (TF)-promoter relationships and microRNA (miR)-target interactions.  ...  Akemi Ohmiya from National Agriculture and Food Research Organization (NARO), Japan for providing ANAC046-OX and ANAC046-SRDX lines. Also, the authors wish to acknowledge Dr. Karolina Mukhtar and Mr.  ... 
doi:10.1038/s41540-018-0071-2 pmid:30181903 pmcid:PMC6119185 fatcat:lhhsvmnvprct7ivck7wvefwbqi

Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile

Min Wang, Jingjun Yan, Xingxing He, Qiang Zhong, Chengye Zhan, Shusheng Li
2016 Biological Research  
A total of seven transcription factors including forkhead box protein M1 (FOXM1) and 30 target genes were revealed in the transcription factor-target gene regulation network.  ...  The up-and down-regulated DEGs were mainly involved in functions like mitotic cell cycle and pathway like cell cycle.  ...  , betweenness centrality and degree centrality respectively in the protein-protein interaction (PPI) network 3 Combined score >0.4 was considered as threshold values of significant difference  ... 
doi:10.1186/s40659-016-0085-4 pmid:27090785 pmcid:PMC4835843 fatcat:rgue2qbjy5h33is623ovgp3hee

Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions

Shubhada R Hegde, Khushbu Pal, Shekhar C Mande
2014 BMC Systems Biology  
Further, dynamics associated with molecular interactions were analysed by studying changing importance of motifs in the composite networks across growth conditions.  ...  We observe a range of importance for network motifs across conditions which can be correlated with a specific function.  ...  Acknowledgements We thank Department of Biotechnology for funding support by Centre of Excellence grant in Microbial Biology BT/01/COE/07/02.  ... 
doi:10.1186/1752-0509-8-26 pmid:24576339 pmcid:PMC4015501 fatcat:kbolfpijwffnvgzjwahpoeoikq

The Effects of Network Neighbours on Protein Evolution

Guang-Zhong Wang, Martin J. Lercher, Johannes Jaeger
2011 PLoS ONE  
Thus, similar expression levels and related functions (as inferred from co-expression and synthetic lethal interactions) seem to explain correlated evolutionary rates of network neighbours across all currently  ...  Similarly, we find correlated rates of evolution of neighbours in networks based on co-expression, metabolism, and synthetic lethal genetic interactions.  ...  Author Contributions Conceived and designed the experiments: MJL GZW. Analyzed the data: GZW MJL. Wrote the paper: MJL GZW.  ... 
doi:10.1371/journal.pone.0018288 pmid:21532755 pmcid:PMC3075247 fatcat:neydfh5msfaqdl4xp2mj7rgpty

Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis [article]

Denise Anna Thiel, Nataša Djurdjevac Conrad, Ria X Peschutter, Heike Siebert, Annalisa Marsico
2018 bioRxiv   pre-print
which combines co-expression analysis with 3D chromatin interaction data.  ...  Recent evidence has shown the importance of both lncRNAs and chromatin interactions in transcriptional regulation.  ...  Acknowledgments The authors kindly acknowledge Leonie Chiara Martens and Martin Vingron for insightful discussions.  ... 
doi:10.1101/331256 fatcat:l7azstqe6nbolkbv3i42ijktye

Topological features of gene regulatory networks predict patterns of natural diversity in environmental response [article]

David L Des Marais, Rafael Guerrero, Jesse R Lasky, Samuel V Scarpino
2016 bioRxiv   pre-print
more peripheral and cold response genes being significantly more central than genes not involved in either response.  ...  Here, we investigated the network topology of genes putatively involved in local adaptation to two abiotic stressors--drought and cold--in Arabidopsis thaliana.  ...  313 314 Methods 315 Co-expression and regulatory networks 316 We used two published datasets on gene expression interactions in in Arabidopsis thaliana. 317 The first dataset was global (i.e. genome-wide  ... 
doi:10.1101/080804 fatcat:twbcw2onojcmpotqtrcl3wtw7a
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