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Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis

Guillem Rigaill, Andrea Rau, Odile Rogier, José Caius, Cathy Maugis-Rabusseau, Ludivine Soubigou-Taconnat, Sébastien Aubourg, Claire Lurin, Marie-Laure Martin-Magniette, Etienne Delannoy
Hence, it provides an evaluation of the key ingredients of the differential analysis , free of the biases associated with the simulation of data using parametric models.  ...  Numerous statistical pipelines are now available for the differential analysis of gene expression measured with RNA-sequencing technology.  ...  Hence, it provides an evaluation of the key ingredients of the differential analysis, free of the biases associated with the simulation of data using parametric models.  ... 

High-Throughput Transcriptome Profiling in Drug and Biomarker Discovery

Xiaonan Yang, Ling Kui, Min Tang, Dawei Li, Kunhua Wei, Wei Chen, Jianhua Miao, Yang Dong
2020 Frontiers in Genetics  
Compared with the traditional RNA-seq, scRNA-seq has higher accuracy and efficiency, especially the single-cell level of gene expression pattern analysis can provide more information for drug and biomarker  ...  A transcriptome is the complete set of all RNAs transcribed by certain tissues or cells at a specific stage of development or physiological condition.  ...  Genetic mutations are the leading cause of autism spectrum disorder (ASD). Duan et al. integrated analyzed RNA-seq and microarray data sets in multiple ASD mouse model.  ... 
doi:10.3389/fgene.2020.00019 pmid:32117438 pmcid:PMC7013098 fatcat:6b6ih77m2jhmpejj7fi77kaopq

Transcriptome analysis of two Pogostemon cablin chemotypes reveals genes related to patchouli alcohol biosynthesis

Wuping Yan, Zhouchen Ye, Shijia Cao, Guanglong Yao, Jing Yu, Dongmei Yang, Ping Chen, Junfeng Zhang, Yougen Wu
2021 PeerJ  
Our transcriptome data also provide a valuable genetic resource for further studies on P. cablin.  ...  PA-type "Nanxiang" (NX) and PO-type "Paixiang" (PX) were analyzed and compared with ribonucleic acid sequencing (RNA-Seq) technology.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj.12025 pmid:34527441 pmcid:PMC8403477 fatcat:nbine5rahjflxk4cwkiavgmbjy

Food authentication from shotgun sequencing reads with an application on high protein powders

Niina Haiminen, Stefan Edlund, David Chambliss, Mark Kunitomi, Bart C. Weimer, Balasubramanian Ganesan, Robert Baker, Peter Markwell, Matthew Davis, B. Carol Huang, Nguyet Kong, Robert J. Prill (+7 others)
2019 npj Science of Food  
Our results demonstrate that DNA/RNA sequencing of food ingredients, combined with a robust analysis, can be used to find contaminants and authenticate food ingredients in a single assay.  ...  To demonstrate this, we developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed to resolve the relative composition of mixtures of eukaryotic species using RNA or  ...  Funding for the total RNA sequencing of high protein powder factory ingredients was provided by Mars, Inc. to B.C.W. with specific interest in metagenomics of the food microbiome.  ... 
doi:10.1038/s41538-019-0056-6 pmid:31754632 pmcid:PMC6863864 fatcat:64x5qa765jfenlcbkv2l3tcelm

Effects of Chinese wolfberry and Astragalus extract on the antioxidant capacity of Tibetan pig liver

Zhuang Hao, Zhen Li, Jinjin Huo, Jiandong Li, Fenghua Liu, Peng Yin, Serena Aceto
2021 PLoS ONE  
Transcriptome sequencing analysis detected 106 differentially expressed genes (DEGs) related to oxidative stress.  ...  The expression levels of key peroxisome biosynthesis genes (e.g., PEX3 and PEX11B) and key antioxidant genes (e.g., CAT and SOD1) were significantly higher in the WAE group than in the control group.  ...  Data statistics and analysis The RNA-seq data were analyzed statistically with DESeq 2 and the other data were analyzed by the one-way T-test in SPSS for Windows (version 20.0; SPSS Inc., Chicago, IL,  ... 
doi:10.1371/journal.pone.0245749 pmid:33503027 fatcat:y6gj4dyzvfb4bdsb7e6ckwj3d4

Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities

Rohit Singh, Brian L Hie, Ashwin Narayan, Bonnie Berger
2021 Genome Biology  
gene expression analysis in the context of spatial variability; and estimate evolutionary pressure on peptide sequences.  ...  We use Schema to infer cell types by integrating gene expression and chromatin accessibility data; demonstrate informative data visualizations that synthesize multiple modalities; perform differential  ...  R.S. wrote the software, A.N. led the mathematical analysis with inputs from R.S. and B.B., and R.S., B.H. and A.N. performed the computational experiments.  ... 
doi:10.1186/s13059-021-02313-2 pmid:33941239 pmcid:PMC8091541 fatcat:xcrinkltwreybhrkwkou5u45c4

Global transcriptome analysis of Huperzia serrata and identification of critical genes involved in the biosynthesis of huperzine A

Mengquan Yang, Wenjing You, Shiwen Wu, Zhen Fan, Baofu Xu, Mulan Zhu, Xuan Li, Youli Xiao
2017 BMC Genomics  
The transcriptome data from this work not only could provide an important resource for further investigating on metabolic pathways in H. serrata, but also shed light on synthetic biology study of HupA.  ...  Moreover, two key classes of CYP450 genes BBE and SLS, with 23 members in total, for modification of the lycopodium alkaloid scaffold in the late two stages of biosynthesis of HupA were further evaluated  ...  Lei Lei for RNA sample preparation assistance.  ... 
doi:10.1186/s12864-017-3615-8 pmid:28330463 pmcid:PMC5361696 fatcat:xgux4qhhefeerndpinhqydtaaq

An Integrated Network, RNA Sequencing, and Experiment Pharmacology Approach Reveals the Active Component, Potential Target, and Mechanism of Gelsemium elegans in the Treatment of Colorectal Cancer

Lin Wang, Hai-li Xu, Jing-wei Liang, Ying-ying Ding, Fan-hao Meng
2020 Frontiers in Oncology  
In the present study, we provide a systematical approach for the identification of effective ingredient and potential target of herbal medicine.  ...  RNA-Seq, enrichment analysis and validation experiment were then further employed to reveal koumine might function in inhibiting Akt/mTOR/HK2 pathway to regulate cell glycolysis and detachment of HK2 from  ...  and performed the analysis. LW and JL contributed to analyze the data and draft the manuscript. FM contributed to the conception, design, and analysis of the manuscript.  ... 
doi:10.3389/fonc.2020.616628 pmid:33425771 pmcid:PMC7786369 fatcat:43hxvy2stfgdzc7qxztnhr4ble

Comprehensive transcriptome profiling of Salvia miltiorrhiza for discovery of genes associated with the biosynthesis of tanshinones and phenolic acids

Wei Zhou, Qiang Huang, Xiao Wu, Zewen Zhou, Mingquan Ding, Min Shi, Fenfen Huang, Shen Li, Yao Wang, Guoyin Kai
2017 Scientific Reports  
The candidate downstream genes and other cytochrome P450s involved in the late steps of tanshinone and phenolic acid biosynthesis pathways were screened from the RNA-seq dataset based on co-expression  ...  This study can provide us a valuable gene resource for elucidating the molecular mechanism of tanshinones and phenolic acids biosynthesis in hairy roots of S. miltiorrhiza.  ...  The RNA-seq and construction of the libraries were performed by Novelbio Biotechnology Corporation (Shanghai, China) and the cDNA library Data analysis and assembly.  ... 
doi:10.1038/s41598-017-10215-2 pmid:28874707 pmcid:PMC5585387 fatcat:26phzk4ltzgqdgpvl7a7khmsi4

Insights into the Regulation of Algal Proteins and Bioactive Peptides Using Proteomic and Transcriptomic Approaches

Lucie Beaulieu
2019 Molecules  
Oceans abound in resources of various kinds for R&D and for commercial applications. Monitoring and bioprospecting allow the identification of an increasing number of key natural resources.  ...  Proteomic and functional genomic approaches based on identifying precursor proteins and bioactive peptides of macroalgae through integrated multi-omics analysis can give insights into their regulation  ...  Conflicts of Interest: The author declares no conflict of interest.  ... 
doi:10.3390/molecules24091708 fatcat:ebe5bi7fmvfiffw3sm3nsvk34m

Personalizing Chinese medicine by integrating molecular features of diseases and herb ingredient information: application to acute myeloid leukemia

Lin Huang, Haichang Li, Duoli Xie, Tieliu Shi, Chengping Wen
2017 OncoTarget  
Pathway analysis and synthetic lethality gene pairs were applied to analyze the dissimilarity, generality and intergroup relations of different groups.  ...  We screened out a set of chemical compounds on basis of AML differential expression genes and chemical-protein interactions and then mapped them to Traditional Chinese Medicine Integrated Database. 415  ...  RESULTS Defining hub targets in DEGs A set of DEGs (596) for AML have been reported based on AML RNA-seq data [16] , which includes 306 down-regulated genes and 290 up-regulated genes (Supplementary  ... 
doi:10.18632/oncotarget.16983 pmid:28454110 pmcid:PMC5522171 fatcat:kjjkyjnt5zhhtnygalac53dhvu

Network-based identification of key master regulators associated with an immune-silent cancer phenotype

Raghvendra Mall, Mohamad Saad, Jessica Roelands, Darawan Rinchai, Khalid Kunji, Hossam Almeer, Wouter Hendrickx, Francesco M Marincola, Michele Ceccarelli, Davide Bedognetti
2021 Briefings in Bioinformatics  
The availability of large genomic datasets offers an opportunity to ascertain key determinants of differential intratumoral immune response.  ...  , and three separate enrichment techniques, including fast gene set enrichment analysis, gene set variation analysis and virtual inference of protein activity by enriched regulon analysis to identify the  ...  A primary ingredient for MRA is to reverse engineer a high quality gene regulatory network (GRN) consisting of TRtarget gene interactions (regulon or gene sets) from RNA-Seq data.  ... 
doi:10.1093/bib/bbab168 pmid:33979427 pmcid:PMC8574720 fatcat:mdogpqnoubbrlgd2l5kyok6bg4

Transcriptome Analysis of Differentially Expressed Genes Involved in Proanthocyanidin Accumulation in the Rhizomes of Fagopyrum dibotrys and an Irradiation-Induced Mutant

Caixia Chen, Ailian Li
2016 Frontiers in Physiology  
The present study aimed to elucidate the molecular mechanism underlying PA accumulation in F. dibotrys by comparing the rhizome transcriptomes of the irradiation-induced mutant and wild-type using RNA-seq  ...  A total of 53,540 unigenes were obtained, of which 29,901 (55.84%) were annotated based on BLAST searches against public databases, and 501 unique sequences were differentially expressed between the two  ...  from RNA-seq data (Ilut et al., 2012) .  ... 
doi:10.3389/fphys.2016.00100 pmid:27047386 pmcid:PMC4796566 fatcat:vgyq3afl4vh6lhdyjo3ifwryhu

Transcriptomic and Metabolomic Differences Between Two Saposhnikovia divaricata (Turcz.) Schischk Phenotypes With Single- and Double-Headed Roots

Tao Zhang, Yuqiu Chen, Qinghe Zhang, Peng Yu, Qiong Li, Weichen Qi, Changbao Chen
2021 Frontiers in Bioengineering and Biotechnology  
Moreover, metabolomic analysis showed that the 126 differentially expressed metabolites were mainly enriched in the biosynthesis of secondary metabolites and phytohormones.  ...  Transcriptomic analysis revealed six significantly differentially expressed genes between the two phenotypes, including five key genes in the flavonoid biosynthesis pathway (4-coumarate-CoA ligase, chalcone  ...  Full-length Transcriptome Assembly from RNA-Seq Data without a Reference Genome. Nat.  ... 
doi:10.3389/fbioe.2021.764093 pmid:34778235 pmcid:PMC8581353 fatcat:thffjknpnzf4jnlwo7edz7ocqu

Anticandidal Potential of Stem Bark Extract from Schima superba and the Identification of Its Major Anticandidal Compound

Chun Wu, Hong-Tan Wu, Qing Wang, Guey-Horng Wang, Xue Yi, Yu-Pei Chen, Guang-Xiong Zhou
2019 Molecules  
Transcriptomic analysis in C. albicans treated with different doses of SSE was conducted through RNA-seq. Average values of 6068 genes and 20,842,500 clean reads were identified from each sample.  ...  This result could be reflected in the irregularly wrinkled morphology of the ruptured cell as revealed through SEM analysis.  ...  Conflicts of Interest: The authors declare no competing financial interest. Molecules 2019, 24, 1587  ... 
doi:10.3390/molecules24081587 fatcat:q4qmdy4jzre2lewiyci36f22xu
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