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RnaSeqSampleSize: real data based sample size estimation for RNA sequencing

Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr
2018 BMC Bioinformatics  
One of the most important and often neglected components of a successful RNA sequencing (RNA-Seq) experiment is sample size estimation.  ...  Results: To solve these issues, we developed a sample size and power estimation method named RnaSeqSampleSize, based on the distributions of gene average read counts and dispersions estimated from real  ...  Acknowledgements The authors wish to thank Michael Smith for providing editorial work and William Gray for providing website support for this manuscript.  ... 
doi:10.1186/s12859-018-2191-5 pmid:29843589 pmcid:PMC5975570 fatcat:ygcf2il4rrei5d42bj2bewtf6q

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments

Ran Bi, Peng Liu
2016 BMC Bioinformatics  
So far, there are very few proposals on sample size calculation for RNA-seq experiments.  ...  Power analysis and sample size calculation are challenging in the context of differential expression analysis with RNA-seq data.  ...  The RnaSeqSampleSize R package [19] could give an estimation of sample size and power by prior real data.  ... 
doi:10.1186/s12859-016-0994-9 pmid:27029470 pmcid:PMC4815167 fatcat:cj5kgy5qovbwvlx5o77olq45lq

Transcriptome sequencing identified hub genes for hepatocellular carcinoma by weighted-gene co-expression analysis

Qi Pan, Xianli Long, Liting Song, Dachun Zhao, Xiaoyuan Li, Dewei Li, Min Li, Jinxue Zhou, Xia Tang, Hong Ren, Keyue Ding
2016 OncoTarget  
In the present study, we performed transcriptome sequencing (mRNA and lncRNA) in liver cancer and cirrhotic tissues of nine HCC patients.  ...  Identification of hub genes for HCC clinical traits has implications for further understanding of the molecular genetic basis of HCC.  ...  First, the number of samples used for RNA-seq was small, and a large sample size is needed to demonstrate the reliability of the results.  ... 
doi:10.18632/oncotarget.9555 pmid:27220887 pmcid:PMC5122405 fatcat:wgqowedygje2tfni5uriembpfu

Adjusted Sample Size Calculation for RNA-seq Data in the Presence of Confounding Covariates

Xiaohong Li, Shesh N. Rai, Eric C. Rouchka, Timothy E. O'Toole, Nigel G. F. Cooper
2021 BioMedInformatics  
Therefore, we introduce confounding covariates for sample size estimation for heterogeneous RNA-seq data.  ...  Although a number of approaches for sample size calculation have been proposed for RNA-seq data, most ignore any potential heterogeneity.  ...  Acknowledgments: The authors gratefully thank the reviewers for the very good suggestions, advice and comments. Conflicts of Interest: The authors declare no conflict interests.  ... 
doi:10.3390/biomedinformatics1020004 fatcat:xzypdpgqufh2tfn6dgxgsaobae

RNA‐seq: Applications and Best Practices [chapter]

Michele Araújo Pereira, Eddie Luidy Imada, Rafael Lucas Muniz Guedes
2017 Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health  
RNA-sequencing (RNA-seq) is the state-of-the-art technique for transcriptome analysis that takes advantage of high-throughput next-generation sequencing.  ...  A complete workflow consists of: (1) experimental design; (2) sample and library preparation; (3) sequencing; and (4) data analysis.  ...  Although RNA-seq provides a precise and accurate estimation of RNA abundance, these findings are still widely required to be further validated through quantitative PCR, also known as qPCR or real-time  ... 
doi:10.5772/intechopen.69250 fatcat:bczbwcjb6rf2dhsthfrzuvi3gm

Genome wide expression analysis of circular RNAs in mammary epithelial cells of cattle revealed difference in milk synthesis

Syed Mudasir Ahmad, Basharat Bhat, Zainab Manzoor, Mashooq Ahmad Dar, Qamar Taban, Eveline M. Ibeagha-Awemu, Nadeem Shabir, Mohd Isfaqul Hussain, Riaz A. Shah, Nazir A. Ganai
2022 PeerJ  
A number of new investigations and research have found that, circRNA; a specific class of non-coding RNAs, is linked with the development of mammary gland and lactation.  ...  Milk is an excellent source of nutrients for humans. Therefore, in order to enhance the quality and production of milk in cattle, it is interesting to examine the underlying mechanisms.  ...  ACKNOWLEDGEMENTS The Dairy Farm of Mountain Livestock Research Institute-Manasbal, SKUAST-K is acknowledged for care and management of the animals. ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj.13029 pmid:35251787 pmcid:PMC8896013 fatcat:67hrcsklhvaxxj4ubdoo6xccdi

Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines

Chen Xie, Cemalettin Bekpen, Sven Künzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Skrabar, Kristian K. Ullrich, Wenyu Zhang, Diethard Tautz, Sushmita Roy
2020 PLoS Computational Biology  
Subsampling analysis of the data reveals that the increase in the number of biological replicates was more important that increasing the sequencing depth to arrive at these results.  ...  For the transcriptome analysis of these stages and tissues, we used a prior power analysis to determine the number of biological replicates and the sequencing depth.  ...  Power analysis for RNA-Seq data RNASeqSampleSize (1.6.0) [11] was used for conducting the power analysis.  ... 
doi:10.1371/journal.pcbi.1008354 pmid:33180766 fatcat:p3besxv35vaonommhywpphzsse

SSizer: Determining the Sample Sufficiency for Comparative Biological Study

Fengcheng Li, Ying Zhou, Xiaoyu Zhang, Jing Tang, Qingxia Yang, Yang Zhang, Yongchao Luo, Jie Hu, Weiwei Xue, Yunqing Qiu, Qiaojun He, Bo Yang (+1 others)
2020 Journal of Molecular Biology  
A sample simulation based on a user-input dataset was performed to expand the data and then determine the sample size required by the particular study.  ...  In sum, SSizer is unique for its ability to comprehensively evaluate whether the sample size is sufficient and determine the required number of samples for the user-input dataset, which, therefore, facilitates  ...  Among these estimation tools, MetaboAnalyst [35] and RnaSeqSampleSize [36] perform well on metabolomic and RNA sequencing data, respectively.  ... 
doi:10.1016/j.jmb.2020.01.027 pmid:32044343 fatcat:dpxz4mwuyjdmze6ercivlq5guq

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines

Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele A Calogero
2018 BMC Bioinformatics  
However, today for reproducing a complex bioinformatics analysis, the raw data and the list of tools used in the workflow could be not enough to guarantee the reproducibility of the results obtained.  ...  One or more Docker images are then defined for a workflow (typically one for each task), while the workflow implementation is handled via R-functions embedded in a package available at github repository  ...  Sample size/statistical power estimation of the experiment and differential expression are calculated respectively via RnaSeqSampleSize [14] and DESeq2 Bioconductor packages [15] .  ... 
doi:10.1186/s12859-018-2296-x pmid:30367595 pmcid:PMC6191970 fatcat:svttxrofbndzla5lduo2ntozfy

Analysis of Salivary Microbiome and Its Association With Periodontitis in Patients With Obstructive Sleep Apnea

Yanlong Chen, Xuehui Chen, Xin Huang, Ying Duan, He Gao, Xuemei Gao
2021 Frontiers in Cellular and Infection Microbiology  
Saliva samples were then collected, and the microbial 16S ribosomal RNA gene was sequenced.  ...  As for periodontal pathogens, the relative abundance of Prevotella was significantly increased in the OSA group.  ...  RnaSeqSampleSize: Real Data Based Sample Size Estimation for RNA Sequencing.  ... 
doi:10.3389/fcimb.2021.752475 pmid:34950605 pmcid:PMC8688821 fatcat:j2qwekelbfe67czrcqa47fghpa

Studying the dawn of de novo gene emergence in mice reveals fast integration of new genes into functional networks [article]

Chen Xie, Cemalettin Bekpen, Sven Künzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Skrabar, Kristian Karsten Ullrich, Diethard Tautz
2019 bioRxiv   pre-print
We have obtained knockouts and analyzed their phenotypes, including a deep transcriptomic analysis, based on a dedicated power analysis.  ...  Here we focus on three loci that have evolved from previously intergenic sequences in the house mouse (Mus musculus) and are not present in its closest relatives.  ...  10 -6 , and n as the real sample size, and rho 691 (2 |log2FoldChange| ), lambda0 (baseMean), and phi0 (dispersion) estimated by DESeq2 (1.14.1) ( RNA-Seq and data analysis 719 The heads of postnatal  ... 
doi:10.1101/510214 fatcat:7pbxehm7fnaxdggfyexq7tyvdi

Comprehensive multi-omics analysis uncovers a group of TGF-β-regulated genes among lncRNA EPR direct transcriptional targets

Ettore Zapparoli, Paola Briata, Martina Rossi, Lorenzo Brondolo, Gabriele Bucci, Roberto Gherzi
2020 Nucleic Acids Research  
Finally, we integrated data derived from ChIRP-Seq, ChIP-Seq as well as RNA-Seq in a comprehensive analysis and we selected a group of bona fide direct transcriptional targets of EPR.  ...  Long non-coding RNAs (lncRNAs) can affect multiple layers of gene expression to control crucial cellular functions.  ...  (Genova branch) for their professional assistance and to Laura Marcenaro and Laura Miscioscia for excellent administrative work.  ... 
doi:10.1093/nar/gkaa628 pmid:32756918 fatcat:3s6zlkjqnzekhp5nc7q2ftuwpy

A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder

Zineb Ammous, Lettie E Rawlins, Hannah Jones, Joseph S Leslie, Olivia Wenger, Ethan Scott, Jim Deline, Tom Herr, Rebecca Evans, Angela Scheid, Joanna Kennedy, Barry A Chioza (+6 others)
2021 PLoS Genetics  
explain the cardinal clinical outcomes in affected individuals, defining potential therapeutic avenues for future research.  ...  Together these data confirm this SNIP1 gene variant as a cause of an autosomal recessive complex neurodevelopmental disorder and provide important insight into the molecular roles of SNIP1, which likely  ...  Program, for providing summary measures from genomic data.  ... 
doi:10.1371/journal.pgen.1009803 pmid:34570759 pmcid:PMC8496849 fatcat:7srtjaqzzvgf3bvtjb3fum67y4

MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV Infection

Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo García, Pablo Ryan Murúa, Juan Macías, Joaquín Cabezas González, Jesús Troya, Juan Antonio Pineda, María Teresa Arias Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa (+5 others)
2019 Journal of Clinical Medicine  
High Throughput sequencing was used to analyze the miRNA profiles from PBMCs of HCV chronic naïve patients (CHC), individuals that spontaneously clarified HCV (SC), and healthy controls (HC).  ...  Acknowledgments: We thank all patients and donors for participating in the current study and all of the nursery team who participated in the collection of patients´samples.  ...  We also thank the reviewers for their valuable suggestions and helpful comments that have helped strenghthen the study.  ... 
doi:10.3390/jcm8060849 pmid:31207946 pmcid:PMC6617112 fatcat:3w3lgae6azbzzbxlpldxwsc7hu

Computational Methods for Interactive and Explorative Study Design and Integration of High-throughput Biological Data [article]

Andreas Friedrich, Universitaet Tuebingen, Kohlbacher, Oliver (Prof. Dr.)
2022
The large sample sizes that modern omics experiments enable, also make it increasingly complicated for scientists to keep track of every sample and the needed annotations.  ...  In this thesis, we develop a multi-tier model for experimental design and a portlet for interactive web-based study design.  ...  for parameter-estimation on real data.  ... 
doi:10.15496/publikation-65976 fatcat:li6kkh2pnzfzvagicujgkpob3y