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Large scale study of anti-sense regulation by differential network analysis

Marc Legeay, Sébastien Aubourg, Jean-Pierre Renou, Béatrice Duval
2018 BMC Systems Biology  
The large-scale differential analysis of apple data that we propose reveals that anti-sense regulation may have an important impact in several cellular stress response mechanisms.  ...  In this work, we propose to explore on a large scale the role of natural anti-sense transcription on gene regulation mechanisms, and we focus our study on apple (Malus domestica) in the context of fruit  ...  0449 for plant production and maintenance, and the ANAN platform of the SFR QuaSaV for microarray facilities access.  ... 
doi:10.1186/s12918-018-0613-7 pmid:30458828 pmcid:PMC6245689 fatcat:nlhwjnsthbddljamx2xfhefv6y

Differential Network Analysis of Anti-sense Regulation [chapter]

Marc Legeay, Béatrice Duval, Jean-Pierre Renou
2017 Lecture Notes in Computer Science  
The aim of our work is to study the role of natural anti-sense transcription on cellular regulation mechanisms.  ...  Secondly, we define the differential network analysis of two extended core networks inferred with and without anti-sense actors.  ...  We thank the Institut de Recherche en Horticulture et Semences teams for providing micro-array data on apple with sense and anti-sense probes.  ... 
doi:10.1007/978-3-319-56154-7_26 fatcat:2ywxzh4cj5c7vib2n74gdptteu

Temporal expression and functional analysis of long non‐coding RNA s in colorectal cancer initiation

Lei Dai, Junshu Li, Zhexu Dong, Yi Liu, Ye Chen, Na Chen, Lin Cheng, Chao Fang, Huiling Wang, Yanhong Ji, Shuang Chen, Xiaolan Su (+10 others)
2019 Journal of Cellular and Molecular Medicine  
Additionally, weighted correlation network analysis (WGCNA) and gene ontology analysis were performed to construct co-expression networks and establish functions of the identified lncRNAs and mRNAs.  ...  In this study, the expression profiles of lncRNAs and mRNAs were determined by microarray at specific tumour stages in an AOM/DSS-induced primary colon cancer model.  ...  A significant feature of scale-free networks is that most nodes have only a few connections, with a few nodes having a large number of connections.  ... 
doi:10.1111/jcmm.14300 pmid:30920116 pmcid:PMC6533480 fatcat:pnkhr7a4brhzblqzl36btne2ge

Comprehensive evaluation of a novel nuclear factor-κB inhibitor, quinoclamine, by transcriptomic analysis

W-Y Cheng, J-C Lien, C-Y Hsiang, S-L Wu, C-C Li, H-Y Lo, J-C Chen, S-Y Chiang, J-A Liang, T-Y Ho
2009 British Journal of Pharmacology  
Quinoclamine-regulated genes interacted with NF-kB or its downstream genes by network analysis.  ...  Conclusion and implications: This study provides a comprehensive evaluation of quinoclamine by transcriptomic analysis.  ...  Medicine and Pharmacy, Department of Health (CCMP96-RD-201 and CCMP97-RD-201), and China Medical University (CMU97-064 and CMU97-CMC-004), Taiwan.  ... 
doi:10.1111/j.1476-5381.2009.00223.x pmid:19422389 pmcid:PMC2721260 fatcat:faatsjtng5dftljxouuheokt7u

Baduanjin exerts anti-diabetic and anti-depression effects by regulating the expression of mRNA, lncRNA, and circRNA

Tian An, Zhong-Chen He, Xin-Qing Zhang, Jun Li, Ai-Ling Chen, Fang Tan, Hong-Dong Chen, Bo-Han Lv, Juan Lian, Si-Hua Gao, Guang-Jian Jiang
2019 Chinese Medicine  
with DD by regulating the dysregulated expression of lncRNA, mRNA, and circRNA.  ...  Subsequently, Gene Ontology (GO) and pathway analysis was performed to investigate the function of differentially expressed mRNAs.  ...  Availability of data and materials The data and materials can be found from the first author and corresponding author.  ... 
doi:10.1186/s13020-019-0225-1 pmid:30733823 pmcid:PMC6359771 fatcat:6ub6o3ci2bhi3nn2a53fautr7i

Network-Based Approach to Identify the Antiproliferative Mechanisms of Bruceine D in Breast Cancer From the Cancer Genome Atlas

Saisai Tian, Rui Jing, Weidong Zhang
2020 Frontiers in Oncology  
pathways and regulating expression of ZFP36, EGR1, and FOS.  ...  In this paper, we aimed to investigate the effect of BD in breast cancer and elucidate the potential mechanism of BD by integrated multiple databases.  ...  As shown in Figure 1 Identification of Modules by Weighted Co-expression Network Analysis Firstly, the genes for co-expression network analysis were selected by differential expression analysis  ... 
doi:10.3389/fonc.2020.01001 pmid:32714860 pmcid:PMC7343963 fatcat:qg7dovyfl5cyjfrspryslqzlsm

An integrated analysis of the competing endogenous RNA network associated of prognosis of stage I lung adenocarcinoma

Yuan Xu, Guofu Lin, Yifei Liu, Xianbin Lin, Hai Lin, Zhifeng Guo, Yingxuan Xu, Qinhui Lin, Shaohua Chen, Jiansheng Yang, Yiming Zeng
2022 BMC Cancer  
Results Of the lncRNAs identified, LINC00639, RP4-676L2.1 and FENDRR were in ceRNA network established by our RNA-sequencing dataset.  ...  The aim of the study is to systematically characterize the lncRNA-associated competing endogenous RNA (ceRNA) network and identify key lncRNAs in the development of stage I lung adenocarcinoma (LUAD).  ...  (sense) and AAC GCT TCA CGA ATT TGC GT (anti-sense).  ... 
doi:10.1186/s12885-022-09290-0 pmid:35183135 pmcid:PMC8857797 fatcat:asqehfvqivdrxn4mn2yql23gnu

Identification of hub molecules of FUS-ALS by Bayesian gene regulatory network analysis of iPSC model: iBRN [article]

Masahiro Nogami, Mitsuru Ishikawa, Atsushi Doi, Osamu Sano, Takafumi Sone, Tetsuya Akiyama, Masashi Aoki, Atsushi Nakanishi, Kazuhiro Ogi, Masato Yano, Hideyuki Okano
2021 bioRxiv   pre-print
Here, we applied a novel platform technology, iBRN, ″Non- biased″ Bayesian gene regulatory network analysis based on induced pluripotent stem cell (iPSC)-derived cell model, to elucidate the molecular  ...  aetiology using transcriptome of iPSC-derived MNs harboring FUSH517D. iBRN revealed ″hub molecules″, which strongly influenced transcriptome network, such as miR-125b-5p-TIMELESS axis and PRKDC for the  ...  Large-scale transcriptome analysis with regular bioinformatics (A, B) PCA analyses of large-scale transcriptome data. The graphics of the PCA are shown.  ... 
doi:10.1101/2021.01.07.425798 fatcat:biwkac33hbaahdhguv3mcitjge

Combined In Silico and In Vivo Analyses Reveal Role of Hes1 in Taste Cell Differentiation

Masato S. Ota, Yoshiyuki Kaneko, Kaori Kondo, Soichi Ogishima, Hiroshi Tanaka, Kazuhiro Eto, Takashi Kondo, Thomas E. Finger
2009 PLoS Genetics  
We used a novel approach to investigate the molecular regulation of taste system development in mice by combining in silico and in vivo analyses.  ...  The sense of taste is of critical importance to animal survival.  ...  We also thank Denis Duboule for comments on the manuscript, and members of the Kondo laboratory for sharing resources. Author Contributions  ... 
doi:10.1371/journal.pgen.1000443 pmid:19343206 pmcid:PMC2655725 fatcat:gjdpi7y5j5dvhonlutli22lktm

Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)

Xuke Lu, Xiugui Chen, Min Mu, Junjuan Wang, Xiaoge Wang, Delong Wang, Zujun Yin, Weili Fan, Shuai Wang, Lixue Guo, Wuwei Ye, Yun Zheng
2016 PLoS ONE  
, three replications), we totally identified 10,820 lncRNAs of high-confidence through five strict steps filtration, of which 9,989 were lincRNAs, 153 were inronic lncRNAs, 678 were anti-sense lncRNAs.  ...  However, the number, characteristics and expression patterns of lncRNAs remain poorly characterized and how these lncRNAs biogenesis are regulated in response to drought stress in cotton are still largely  ...  Acknowledgments This project was supported by grants from the Genetically modified organisms breeding (2014 ZX0800504B).  ... 
doi:10.1371/journal.pone.0156723 pmid:27294517 pmcid:PMC4905672 fatcat:zbkbi22dlbefhbwufkwqmu7xsu

Complete Transcriptome Profiling of Normal and Age-Related Macular Degeneration Eye Tissues Reveals Dysregulation of Anti-Sense Transcription

Eun Ji Kim, Gregory R. Grant, Anita S. Bowman, Naqi Haider, Harini V. Gudiseva, Venkata Ramana Murthy Chavali
2018 Scientific Reports  
The transcriptome analysis reveals a highly significant and consistent impact on anti-sense transcription as well as moderate changes in the regulation of non-coding (sense) RNA.  ...  Hundreds of genes that do not express anti-sense transcripts in normal PR and PRCS demonstrate significant anti-sense expression in AMD in all patient samples.  ...  The magnitude of differential anti-sense expression observed in our study suggests that anti-sense transcription could provide another level of gene regulation in addition to post-translational and transcription  ... 
doi:10.1038/s41598-018-21104-7 pmid:29445097 pmcid:PMC5813239 fatcat:yyolgmmtvnbejkuq57bpfuwmnm

Synergizing Genomic Analysis With Biological Knowledge to Identify and Validate Novel Genes in Pancreatic Development

Suparna A. Sarkar, Catherine E. Lee, Hannah Tipney, Anis Karimpour-Fard, Jason D. Dinella, Kirstine Juhl, Jay A. Walters, John C. Hutton, Lawrence E. Hunter
2012 Pancreas  
Objective-This study investigated the utility of advanced computational techniques to large scale-genome based data to identify novel genes that govern murine pancreatic development.  ...  The molecular mechanism of pancreatic morphogenesis and differentiation is a fundamental enigma during pancreas development.  ...  The authors are grateful to Jan Kraus, PhD from University of Colorado Denver for providing Cbs monoclonal antibody. Dr. Chris Wright, PhD is thanked for the Pdx1 antibody.  ... 
doi:10.1097/mpa.0b013e31823d0160 pmid:22450367 pmcid:PMC3387325 fatcat:teeospqqlbck3dgbz3xh4xn4p4

Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response

Yu Gao, Laurence Flori, Jérome Lecardonnel, Diane Esquerré, Zhi-Liang Hu, Angélique Teillaud, Gaëtan Lemonnier, Francois Lefèvre, Isabelle P Oswald, Claire Rogel-Gaillard
2010 BMC Genomics  
Transcriptome analysis revealed that ten times more genes were differentially expressed after PMA/ionomycin stimulation than after LPS stimulation.  ...  Repression of MHC class I genes was observed after PMA/ionomycin stimulation despite an up-regulation of the gene cascade involved in peptide processing.  ...  Four probes are up-regulated (anti-sense sequences of BAT3, IER3, EGFL8 and PSMB9) and nine probes are down-regulated (anti-sense sequences of OLF42-3, STK19, LSM2, AIF1, STK19, BAT1, RPP21, SKIV2L and  ... 
doi:10.1186/1471-2164-11-292 pmid:20459780 pmcid:PMC2881026 fatcat:7eqde3jaffcgjo5eys3j7chcdm

Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

Chong Feng, Lei Cui, Zhen Jin, Lei Sun, Xiaoyan Wang, Xinshu Chi, Qian Sun, Siyu Lian
2022 BMC Genomic Data  
In this study, we constructed gene co-expression networks to identify key modules and hub genes involved in the pathogenesis of EC.  ...  Functional enrichment analysis showed that the MEturquoise module was associated with the GO biological process terms of transcription from RNA polymerase II promoter, positive regulation of male gonad  ...  , and download of large-scale cancer genomics datasets.  ... 
doi:10.1186/s12863-022-01028-y pmid:35123404 pmcid:PMC8818217 fatcat:4k2x2cbaxfaadi7lrimfabzd5y

SLE Peripheral Blood B Cell, T Cell and Myeloid Cell Transcriptomes Display Unique Profiles and Each Subset Contributes to the Interferon Signature

Amy M. Becker, Kathryn H. Dao, Bobby Kwanghoon Han, Roger Kornu, Shuchi Lakhanpal, Angela B. Mobley, Quan-Zhen Li, Yun Lian, Tianfu Wu, Andreas M. Reimold, Nancy J. Olsen, David R. Karp (+8 others)
2013 PLoS ONE  
The goal of the current study was to assess the gene expression profiles of isolated leukocyte subsets obtained from SLE patients.  ...  Only 4.4% (21) of the 474 total transcripts, many associated with the IFN signature, were shared by all three subsets.  ...  with data and statistical analysis and Jacob Orme for support with graphics.  ... 
doi:10.1371/journal.pone.0067003 pmid:23826184 pmcid:PMC3691135 fatcat:7jjbn2spcnesbk24plv3llkqna
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