Differential analysis on stratified spaces

ABSTRACT This paper reintroduces economist John Maurice Clark to the accounting academic community while investigating his role in the development of managerial accounting. Clark was a prominent American economist during the early half of the 20th century, whose first major book, Studies in the Economics of Overhead Costs (Clark 1923a), has been described by diverse authors as foundational to the field of managerial accounting, especially overhead estimation and differential analysis. An overview of Clark's life is provided, followed by discussion of the importance of his work to accounting. Citation counts of his work in various accounting journals reveal that although widely referenced by accounting scholars for a short time after the publication of Overhead Costs, his name then disappeared from the literature, and indicates that his work is underappreciated. The paper discusses why this lacuna in accounting history is significant, and gives possible explanations for why Clark's work has been overlooked.

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ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400185 ◽

2019 ◽

Vol 9 (7) ◽

pp. 2089-2096 ◽

Cited By ~ 4

Author(s):

Stephany Orjuela ◽

Ruizhu Huang ◽

Katharina M. Hembach ◽

Mark D. Robinson ◽

Charlotte Soneson

Keyword(s):

Differential Analysis ◽

Rna Seq

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D2A: A Dataset Built for AI-Based Vulnerability Detection Methods Using Differential Analysis

2021 IEEE/ACM 43rd International Conference on Software Engineering: Software Engineering in Practice (ICSE-SEIP) ◽

10.1109/icse-seip52600.2021.00020 ◽

2021 ◽

Author(s):

Yunhui Zheng ◽

Saurabh Pujar ◽

Burn Lewis ◽

Luca Buratti ◽

Edward Epstein ◽

...

Keyword(s):

Detection Methods ◽

Differential Analysis ◽

Vulnerability Detection

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DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

International Journal of Molecular Sciences ◽

10.3390/ijms22031399 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1399

Author(s):

Salim Ghannoum ◽

Waldir Leoncio Netto ◽

Damiano Fantini ◽

Benjamin Ragan-Kelley ◽

Amirabbas Parizadeh ◽

...

Keyword(s):

Single Cell ◽

Biomarker Discovery ◽

Enrichment Analysis ◽

Myxoid Liposarcoma ◽

R Package ◽

Differential Analysis ◽

A Cell ◽

Reproducible Analysis ◽

Transcriptomic Level ◽

User Friendly

The growing attention toward the benefits of single-cell RNA sequencing (scRNA-seq) is leading to a myriad of computational packages for the analysis of different aspects of scRNA-seq data. For researchers without advanced programing skills, it is very challenging to combine several packages in order to perform the desired analysis in a simple and reproducible way. Here we present DIscBIO, an open-source, multi-algorithmic pipeline for easy, efficient and reproducible analysis of cellular sub-populations at the transcriptomic level. The pipeline integrates multiple scRNA-seq packages and allows biomarker discovery with decision trees and gene enrichment analysis in a network context using single-cell sequencing read counts through clustering and differential analysis. DIscBIO is freely available as an R package. It can be run either in command-line mode or through a user-friendly computational pipeline using Jupyter notebooks. We showcase all pipeline features using two scRNA-seq datasets. The first dataset consists of circulating tumor cells from patients with breast cancer. The second one is a cell cycle regulation dataset in myxoid liposarcoma. All analyses are available as notebooks that integrate in a sequential narrative R code with explanatory text and output data and images. R users can use the notebooks to understand the different steps of the pipeline and will guide them to explore their scRNA-seq data. We also provide a cloud version using Binder that allows the execution of the pipeline without the need of downloading R, Jupyter or any of the packages used by the pipeline. The cloud version can serve as a tutorial for training purposes, especially for those that are not R users or have limited programing skills. However, in order to do meaningful scRNA-seq analyses, all users will need to understand the implemented methods and their possible options and limitations.

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Sex-Biased lncRNA Signature in Fetal Growth Restriction (FGR)

Cells ◽

10.3390/cells10040921 ◽

2021 ◽

Vol 10 (4) ◽

pp. 921

Author(s):

Aleksandra Lipka ◽

Jan Pawel Jastrzebski ◽

Lukasz Paukszto ◽

Karol Gustaw Makowczenko ◽

Elzbieta Lopienska-Biernat ◽

...

Keyword(s):

Fetal Growth ◽

Fetal Growth Restriction ◽

Target Genes ◽

Active Regions ◽

Bioinformatic Analysis ◽

Growth Restriction ◽

Differentially Expressed ◽

Circular Rnas ◽

Differential Analysis ◽

Protein Coding

Impaired fetal growth is one of the most important causes of prematurity, stillbirth and infant mortality. The pathogenesis of idiopathic fetal growth restriction (FGR) is poorly understood but is thought to be multifactorial and comprise a range of genetic causes. This research aimed to investigate non-coding RNAs (lncRNAs) in the placentas of male and female fetuses affected by FGR. RNA-Seq data were analyzed to detect lncRNAs, their potential target genes and circular RNAs (circRNAs); a differential analysis was also performed. The multilevel bioinformatic analysis enabled the detection of 23,137 placental lncRNAs and 4263 of them were classified as novel. In FGR-affected female fetuses’ placentas (ff-FGR), among 19 transcriptionally active regions (TARs), five differentially expressed lncRNAs (DELs) and 12 differentially expressed protein-coding genes (DEGs) were identified. Within 232 differentially expressed TARs identified in male fetuses (mf-FGR), 33 encompassed novel and 176 known lncRNAs, and 52 DEGs were upregulated, while 180 revealed decreased expression. In ff-FGR ACTA2-AS1, lncRNA expression was significantly correlated with five DEGs, and in mf-FGR, 25 TARs were associated with DELs correlated with 157 unique DEGs. Backsplicing circRNA processes were detected in the range of H19 lncRNA, in both ff- and mf-FGR placentas. The performed global lncRNAs characteristics in terms of fetal sex showed dysregulation of DELs, DEGs and circRNAs that may affect fetus growth and pregnancy outcomes. In female placentas, DELs and DEGs were associated mainly with the vasculature, while in male placentas, disturbed expression predominantly affected immune processes.

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Insights into the Mechanism of Bovine Spermiogenesis Based on Comparative Transcriptomic Studies

Animals ◽

10.3390/ani11010080 ◽

2021 ◽

Vol 11 (1) ◽

pp. 80

Author(s):

Xin Li ◽

Chenying Duan ◽

Ruyi Li ◽

Dong Wang

Keyword(s):

Gene Expression ◽

Semen Quality ◽

Regulation Of Gene Expression ◽

Physiological Mechanism ◽

Interaction Network ◽

Seminiferous Tubules ◽

Differential Analysis ◽

Epididymal Sperm ◽

Bioinformatics Analyses ◽

Acrosome Formation

To reduce subfertility caused by low semen quality and provide theoretical guidance for the eradication of human male infertility, we sequenced the bovine transcriptomes of round, elongated spermatids and epididymal sperms. The differential analysis was carried out with the reference of the mouse transcriptome, and the homology trends of gene expression to the mouse were also analysed. First, to explore the physiological mechanism of spermiogenesis that profoundly affects semen quality, homological trends of differential genes were compared during spermiogenesis in dairy cattle and mice. Next, Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment, protein–protein interaction network (PPI network), and bioinformatics analyses were performed to uncover the regulation network of acrosome formation during the transition from round to elongated spermatids. In addition, processes that regulate gene expression during spermiogenesis from elongated spermatid to epididymal sperm, such as ubiquitination, acetylation, deacetylation, and glycosylation, and the functional ART3 gene may play important roles during spermiogenesis. Therefore, its localisation in the seminiferous tubules and epididymal sperm were investigated using immunofluorescent analysis, and its structure and function were also predicted. Our findings provide a deeper understanding of the process of spermiogenesis, which involves acrosome formation, histone replacement, and the fine regulation of gene expression.

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Replicate sequencing libraries are important for quantification of allelic imbalance

Nature Communications ◽

10.1038/s41467-021-23544-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Asia Mendelevich ◽

Svetlana Vinogradova ◽

Saumya Gupta ◽

Andrey A. Mironov ◽

Shamil R. Sunyaev ◽

...

Keyword(s):

Allelic Imbalance ◽

False Positive Rate ◽

Error Rates ◽

Differential Analysis ◽

Rna Seq ◽

Specific Expression ◽

Technical Noise ◽

Specific Analysis ◽

Positive Rate ◽

Allele Specific

AbstractA sensitive approach to quantitative analysis of transcriptional regulation in diploid organisms is analysis of allelic imbalance (AI) in RNA sequencing (RNA-seq) data. A near-universal practice in such studies is to prepare and sequence only one library per RNA sample. We present theoretical and experimental evidence that data from a single RNA-seq library is insufficient for reliable quantification of the contribution of technical noise to the observed AI signal; consequently, reliance on one-replicate experimental design can lead to unaccounted-for variation in error rates in allele-specific analysis. We develop a computational approach, Qllelic, that accurately accounts for technical noise by making use of replicate RNA-seq libraries. Testing on new and existing datasets shows that application of Qllelic greatly decreases false positive rate in allele-specific analysis while conserving appropriate signal, and thus greatly improves reproducibility of AI estimates. We explore sources of technical overdispersion in observed AI signal and conclude by discussing design of RNA-seq studies addressing two biologically important questions: quantification of transcriptome-wide AI in one sample, and differential analysis of allele-specific expression between samples.

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Identification of prognostic biomarkers related to the tumor microenvironment in thyroid carcinoma

Scientific Reports ◽

10.1038/s41598-021-90538-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jun-wei Du ◽

Guo-quan Li ◽

Yang-sen Li ◽

Xin-guang Qiu

Keyword(s):

Tumor Microenvironment ◽

Thyroid Carcinoma ◽

Differentially Expressed Genes ◽

Essential Role ◽

Endocrine Tumor ◽

Differentially Expressed ◽

Differential Analysis ◽

Additional Information ◽

Cerna Network ◽

Immune Score

AbstractThyroid Carcinoma (THCA) is the most common endocrine tumor that is mainly treated using surgery and radiotherapy. In addition, immunotherapy is a recently developed treatment option that has played an essential role in the management of several types of tumors. However, few reports exist on the use of immunotherapy to treat THCA. The study downloaded the miRNA, mRNA and lncRNA data for THCA patients from the TCGA database (https://portal.gdc.cancer.gov/). Thereafter, the tumor samples were divided into cold and hot tumors, based on the immune score of the tumor microenvironment. Moreover, the differentially expressed lncRNAs and miRNAs were obtained. Finally, the study jointly constructed a ceRNA network through differential analysis of the mRNA data for cold and hot tumors. The study first assessed the level of immune infiltration in the THCA tumor microenvironment then divided the samples into cold and hot tumors, based on the immune score. Additionally, a total of 568 up-regulated and 412 down-regulated DEGs were screened by analyzing the differences between hot and cold tumors. Thereafter, the study examined the differentially expressed genes for lncRNA and miRNA. The results revealed 629 differentially expressed genes related to lncRNA and 114 associated with miRNA. Finally, a ceRNA network of the differentially expressed genes was constructed. The results showed a five-miRNA hubnet, i.e., hsa-mir-204, hsa-mir-128, hsa-mir-214, hsa-mir-150 and hsa-mir-338. The present study identified the immune-related mRNA, lncRNA and miRNA in THCA then constructed a ceRNA network. These results are therefore important as they provide more insights on the immune mechanisms in THCA. The findings also provides additional information for possible THCA immunotherapy.

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Harmonic forms and cohomology of singular stratified spaces

Bulletin des Sciences Mathématiques ◽

10.1016/j.bulsci.2006.09.001 ◽

2007 ◽

Vol 131 (5) ◽

pp. 422-456

Author(s):

Vincenzo Ancona ◽

Bernard Gaveau ◽

Masami Okada

Keyword(s):

Harmonic Forms ◽

Stratified Spaces

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