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Poisson factor models with applications to non-normalized microRNA profiling

Seonjoo Lee, Pauline E. Chugh, Haipeng Shen, R. Eberle, Dirk P. Dittmer
2013 Computer applications in the biosciences : CABIOS  
We develop an efficient algorithm for estimating the Poisson factor model, entitled Poisson Singular Value Decomposition with Offset (PSVDOS).  ...  Through analysis of an miRNA profiling experiment, we further illustrate that our model achieves insightful dimension reduction of the miRNA profiles of 18 samples: the extracted factors lead to more accurate  ...  An interesting direction for future research is to develop an appropriate factor model to address the overdispersion. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btt091 pmid:23428639 pmcid:PMC3634185 fatcat:omt3povndbgfhgvrkh5w7okf6y

Poisson factor models with applications to non-normalized microRNA profiling

Dirk P. Dittmer, Pauline E. Chugh, R. Eberle, Haipeng Shen, Seonjoo Lee
2013
Our primary motivating application is to identify different viral infections based on the induced change in the host miRNA profile.  ...  across samples that require appropriate normalization.  ...  An interesting direction for future research is to develop an appropriate factor model to address the overdispersion. Conflict of Interest: none declared.  ... 
doi:10.17615/5h21-yh38 fatcat:7tihzdqwbbeypfovn6jcxf3zxe

A Log-Linear Graphical Model for Inferring Genetic Networks from High-Throughput Sequencing Data [article]

Genevera I. Allen, Zhandong Liu
2012 arXiv   pre-print
A case study on breast cancer microRNAs, a novel application of graphical models, finds known regulators of breast cancer genes and discovers novel microRNA clusters and hubs that are targets for future  ...  Additionally, we develop a fast parallel algorithm, an approach we call the Poisson Graphical Lasso, permitting us to fit our graphical model to high-dimensional genomic data sets.  ...  graphical models and in the application of these to gene expression and microRNA expression networks. ( b ) b For b = 1, . . .  ... 
arXiv:1204.3941v2 fatcat:apxu24mtyre7zdq5u6gfrc6bti

NanoStringDiff: a novel statistical method for differential expression analysis based on NanoString nCounter data

Hong Wang, Craig Horbinski, Hao Wu, Yinxing Liu, Shaoyi Sheng, Jinpeng Liu, Heidi Weiss, Arnold J. Stromberg, Chi Wang
2016 Nucleic Acids Research  
expression levels without amplification, digital readout and superior applicability to formalin fixed paraffin embedded samples.  ...  Data normalization is incorporated in the model framework through data normalization parameters, which are estimated from positive controls, negative controls and housekeeping genes embedded in the nCounter  ...  The NanoString nCounter data, referred to as the Horbinski data, are available at Gene Expression Omnibus under accession number GSE80821.  ... 
doi:10.1093/nar/gkw677 pmid:27471031 pmcid:PMC5175344 fatcat:ng6aj7ste5gdfjpqbn2b4cv4ja

Importance of Micrornas in Human Cancer Development: A Molecular Analytical Approach

Ahmed FE, Gouda MM, Ahmed NC
2021 Clinics of Surgery  
For qRT-PCR applications, the tools include: a) Effective method of microRNA isolation from samples; b) RT-qPCR reagents optimized for microRNA detection; c) Assays specific to the microRNAs of interest  ...  non-to the invasive stages of various types of human cancers, as detailed in this review below.  ...  To account for wells that may have received more than one molecule of the target sequence, a correction factor is applied using the Poisson model.  ... 
doi:10.47829/cos.2021.6401 fatcat:ia5taaywgzdk7o3n7cuak46ezy

CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing [article]

Yuchao Jiang, Rujin Wang, Eugene Urrutia, Ioannis N Anastopoulos, Katherine L Nathanson, Nancy R Zhang
2017 bioRxiv   pre-print
We describe CODEX2, a statistical framework for full-spectrum CNV profiling that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with  ...  High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods, but suffers from biases and artifacts that  ...  Lee S, Chugh PE, Shen H, Eberle R, Dittmer DP: Poisson factor models with applications to non-585 normalized microRNA profiling. Bioinformatics 2013, 29:1105-1111.  ... 
doi:10.1101/211698 fatcat:olj26gryqfgtphwwuarh4fmwle

Intrinsic Noise of microRNA-Regulated Genes and the ceRNA Hypothesis

Javad Noorbakhsh, Alex H. Lang, Pankaj Mehta, Barbara Bardoni
2013 PLoS ONE  
We use a quantitative model to study gene regulation by inhibitory microRNAs and compare it to gene regulation by prokaryotic small non-coding RNAs (sRNAs).  ...  Our model uses a combination of analytic techniques as well as computational simulations to calculate the mean-expression and noise profiles of genes regulated by both microRNAs and sRNAs.  ...  Our model is also applicable to plant microRNAs where microRNAs bind strongly to regulated mRNAs [34] .  ... 
doi:10.1371/journal.pone.0072676 pmid:23991139 pmcid:PMC3749174 fatcat:qlphe5iu4fg7vmtxeioqqqsukq

Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls

Daniela Witten, Robert Tibshirani, Sam Gu, Andrew Fire, Weng-Onn Lui
2010 BMC Biology  
We tested several computational approaches for the analysis of class differences between high throughput sequencing datasets and describe a novel application of a log linear model that has provided the  ...  Analysis of the resulting sequences (42 million in total) defined 64 new human microRNA (miRNA) genes.  ...  In order to identify miRNAs that were differentially expressed between normal and tumour samples, we developed a Poisson log-linear model.  ... 
doi:10.1186/1741-7007-8-58 pmid:20459774 pmcid:PMC2880020 fatcat:ifslgcjjgneh7da62qg74ho3d4

Bromodomain and extra-terminal domain inhibition modulates the expression of pathologically relevant microRNAs in diffuse large B-cell lymphoma

Afua A. Mensah, Luciano Cascione, Eugenio Gaudio, Chiara Tarantelli, Riccardo Bomben, Elena Bernasconi, Domenico Zito, Andrea Lampis, Jens C. Hahne, Andrea Rinaldi, Anastasios Stathis, Emanuele Zucca (+5 others)
2018 Haematologica  
For the Nanostring nCounter, raw expression data were log-transformed and normalized by the quantile method after application of manufacturer-supplied correction factors.  ...  MicroRNA quantification with TaqMan microRNA assays Profiling results for selected miRNAs were validated using the following TaqMan MicroRNA Assays (Applied Biosystems): hsa-miR-96-5p, assay ID: 000186  ... 
doi:10.3324/haematol.2018.191684 pmid:30076183 fatcat:opogcgpecveozpumfvbgah7rce

SCOPE: a normalization and copy number estimation method for single-cell DNA sequencing [article]

Rujin Wang, Dan-Yu Lin, Yuchao Jiang
2019 bioRxiv   pre-print
The main features of SCOPE include: (i) a Poisson latent factor model for normalization, which borrows information across cells and regions to estimate bias, using negative control cells identified by  ...  cell-specific Gini coefficients; (ii) modeling of GC content bias using an expectation-maximization algorithm embedded in the normalization step, which accounts for the aberrant copy number changes that  ...  Poisson factor models with 668 applications to non-normalized microRNA profiling. Bioinformatics 29, 1105-1111. 43.  ... 
doi:10.1101/594267 fatcat:6msmj4d73jcmzell2h66rnxlou

MicroRNAs in the pathogeny of chronic lymphocytic leukaemia

Milena S. Nicoloso, Thomas J. Kipps, Carlo M. Croce, George A. Calin
2007 British Journal of Haematology  
MicroRNAs (miRNAs) have been linked to the initiation and progression of chronic lymphocytic leukaemia (CLL).  ...  The main molecular alterations are represented by variations in gene expression, usually mild and with consequences for a vast number of target protein-coding genes.  ...  We apologize to our colleagues whose work was not cited because of space limitations.  ... 
doi:10.1111/j.1365-2141.2007.06868.x pmid:18021085 fatcat:rx5fvv5dzfhdje3uucy3vapzgy

Modeling bias and variation in the stochastic processes of small RNA sequencing

Christos Argyropoulos, Alton Etheridge, Nikita Sakhanenko, David Galas
2017 Nucleic Acids Research  
Empirical bias correction factors appear to be nearly constant over at least one and up to four orders of magnitude of total RNA input and independent of sample composition.  ...  empirical correction factors for ligase bias.  ...  Poisson model.  ... 
doi:10.1093/nar/gkx199 pmid:28369495 pmcid:PMC5499834 fatcat:qtcbisikqndixpxbrw3oaf67vy

Digital PCR Absolute Quantification of Micro RNAs for The Noninvasive Diagnostic Screening of Colon Cancer in Humans

Farid E Ahmed
2018 Biomedical Journal of Scientific & Technical Research  
The discovery of small noncoding protein sequences, 17-27 nucleotides long RNAs (such as microRNAs), has opened new opportunities for a non-invasive test for early diagnosis of many cancers.  ...  Profiles of miRNA expression differ between normal tissues and tumor types, and evidence suggests that miRNA expression profiles can cluster similar tumor types together more accurately than expression  ...  To account for wells that may have received more than one molecule of the target sequence, a correction factor is applied using the Poisson model.  ... 
doi:10.26717/bjstr.2018.09.001778 fatcat:pvfrc7a3ufbajawdq7ixdkgobu

Which statistical significance test best detects oncomiRNAs in cancer tissues? An exploratory analysis

Wei Tang, Zhijun Liao, Quan Zou
2016 OncoTarget  
MicroRNAs(miRNAs) often exert their oncogenic and tumor suppressor functions by suppressing protein-coding genes expressions in cancers and thus have a strong association with cancers' generation, development  ...  experimentally validated differentially expressed miRNAs, and Infer microRNA-disease association database, which contains the potential diseaseassociated miRNAs by network forecasting.  ...  The NB model corrects the overdispersion problem in RNA sequence data by an additional term in the variance of the Poisson model.  ... 
doi:10.18632/oncotarget.12828 pmid:27784000 pmcid:PMC5356763 fatcat:ca2oopydibdxtevjsuyjgingxq

CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing

Yuchao Jiang, Rujin Wang, Eugene Urrutia, Ioannis N. Anastopoulos, Katherine L. Nathanson, Nancy R. Zhang
2018 Genome Biology  
We describe CODEX2, as a statistical framework for full-spectrum CNV profiling that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with  ...  High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods but suffers from biases and artifacts that  ...  [30] apply a similar Poisson factor approach to the non-normalized microRNA sequencing data. Chen et al.  ... 
doi:10.1186/s13059-018-1578-y pmid:30477554 fatcat:aiwxwdtfffap7d3btijhrxxpzm
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