Tag: wilcoxon

Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

Continue Reading Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Subsetting DESEQ2 VST Microbiome Data

Subsetting DESEQ2 VST Microbiome Data 1 @f8d5630d Last seen 16 hours ago Germany Hello there, the question is a bit off topic I am currently using DESEQ2 to normalize 16S microbiome data as advised several times in the recent literature. Currently I am facing the problem that I have 16S…

Continue Reading Subsetting DESEQ2 VST Microbiome Data

Effects of terfenadine and diphenhydramine on the CYP2D6 activity in healthy volunteers.

The aim of this study was to investigate the effects of two antihistaminic drugs, terfenadine and diphenhydramine on CYP2D6 activity by using debrisoquine as a model substrate. The study was carried out as an in vivo single-dose study in 12 young, healthy men. All volunteers had previously been identified as…

Continue Reading Effects of terfenadine and diphenhydramine on the CYP2D6 activity in healthy volunteers.

Vertical stratification of the air microbiome in the lower troposphere

Significance Large-scale meteorological and biological data demonstrate the vertical stratification of airborne biomass. The previously described diel cycle of airborne microorganisms is shown to disappear at height. Atmospheric turbulence and stratification are shown to be defining factors for the scale and boundaries, dynamics, and natural variability of airborne biomass, resulting…

Continue Reading Vertical stratification of the air microbiome in the lower troposphere

Identification of a four-gene signature & PTC.

Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…

Continue Reading Identification of a four-gene signature & PTC.

The Identification of Prognostic and Metastatic Alternative Splicing in Skin Cutaneous Melanoma

Skin cutaneous melanoma (SKCM) is a type of highly invasive cancer originated from melanocytes. It is reported that aberrant alternative splicing (AS) plays an important role in the neoplasia and metastasis of many types of cancer. Therefore, we investigated whether ASEs of pre-RNA have such an influence on the prognosis…

Continue Reading The Identification of Prognostic and Metastatic Alternative Splicing in Skin Cutaneous Melanoma

Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

Continue Reading Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice

O304 treatment prevents islet gene expression signature changes induced by HFD We have previously demonstrated that the AMPK activator O304 improves blood glucose homeostasis in both human T2D subjects as well as in high-fat diet induced obese and diabetic mouse models. In the present study, we have now analysed the…

Continue Reading Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice

Crosstalk between Venous Thromboembolism and Periodontal Diseases: A Bioinformatics Analysis

This article was originally published here Dis Markers. 2021 Dec 10;2021:1776567. doi: 10.1155/2021/1776567. eCollection 2021. ABSTRACT BACKGROUND: This current study applied bioinformatics analysis to reveal the crosstalk between venous thromboembolism (VTE) and periodontitis, as well as the potential role of immune-related genes in this context. METHODS: Expression data were downloaded…

Continue Reading Crosstalk between Venous Thromboembolism and Periodontal Diseases: A Bioinformatics Analysis

Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

Continue Reading Adrenal aldosterone-producing adenoma | IJGM

The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines | Clinical Epigenetics

Methylation analysis pipelines The ENmix pipeline performs data preprocessing in a stepwise way, including ENmix background correction [1], RELIC dye bias correction [3], optional inter-array normalization, RCP probe-type bias correction [2], quality control, filtering of low-quality data points, and imputation. ENmix background correction employs a mixture of exponential and truncated…

Continue Reading The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines | Clinical Epigenetics

Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…

Continue Reading Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

Analysis of Community Composition of Bacterioplankton in Changle Seawater in China by Illumina Sequencing Combined with Bacteria Culture

Orthop Surg. 2021 Nov 24. doi: 10.1111/os.13060. Online ahead of print. ABSTRACT OBJECTIVES: To characterize the abundance and relative composition of seawater bacterioplankton communities in Changle city using Illumina MiSeq sequencing and bacterial culture techniques. METHODS: Seawater samples and physicochemical factors were collected from the coastal zone of Changle city…

Continue Reading Analysis of Community Composition of Bacterioplankton in Changle Seawater in China by Illumina Sequencing Combined with Bacteria Culture

Diagnostic markers of AIDS combined with TM infection

Introduction The prevalence of Human immunodeficiency virus/Acquired Immune Deficiency Syndrome (HIV/AIDS) is still a public health problem that threatens the health of all human beings. According to the latest report of the World Health Organization, in the end of 2019, there were 38 million patients with human immunodeficiency virus/acquired immunodeficiency…

Continue Reading Diagnostic markers of AIDS combined with TM infection

An evolutionary functional genomics approach identifies novel candidate regions involved in isoniazid resistance in Mycobacterium tuberculosis

Functional genomics allows for detection of resistance-associated genomic regions We generated a highly saturated M. tuberculosis H37Rv pool with over 100,000 different transposon-insertion mutants following the protocol by Long et al.8. Using TnSeq, we found 58,389 out of 74,603 possible insertion sites had at least one read, meaning a saturation…

Continue Reading An evolutionary functional genomics approach identifies novel candidate regions involved in isoniazid resistance in Mycobacterium tuberculosis

Asc-Seurat: analytical single-cell Seurat-based web application | BMC Bioinformatics

To demonstrate Asc-Seurat’s functionalities, we analyzed the publicly available 10× Genomics’ 3k Peripheral Blood Mononuclear Cells (PBMC) dataset [26], showcasing the analysis of an individual sample. In addition, we used a second PBMC dataset to demonstrate the analysis integrating multiple samples in Asc-Seurat. The second PBMC dataset was generated by Hang…

Continue Reading Asc-Seurat: analytical single-cell Seurat-based web application | BMC Bioinformatics

Frontiers | Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

Introduction Corn and soybean meal are the main components of high energy and high protein diets for pigs and are also the main raw materials of food products for human consumption, fermentation, and bioenergy industry (Sevillano et al., 2018). As the arable land of food crops was limited whereas the…

Continue Reading Frontiers | Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

Chapter 9 Differential abundance analysis

Here, we analyse abundances with three different methods: Wilcoxon test (CLR), DESeq2, and ANCOM-BC. All of these test statistical differences between groups. We will analyse Genus level abundances. We might want to first perform prevalence filtering to reduce the amount of multiple tests. In this particular dataset, all genera pass…

Continue Reading Chapter 9 Differential abundance analysis

best practice for applying FDR to highly similar group DEG analysis

hi, i am grad student who is mid of master’s degree. one of my project is revealing some genes that differentially expressed between cancer that has small size and do not lymph node metastasis and cancer that has small size and do lymph node metastasis. i’d done sampling from 10…

Continue Reading best practice for applying FDR to highly similar group DEG analysis

Factors influencing multidrug-resistant tuberculosis | IDR

Introduction Pediatric tuberculosis (TB) is a significant global health threat and is one of the top ten causes of death in children.1 Globally, in 2019, an estimated 10.0 million people fell ill with TB, with children (aged under 15 years old) accounting for 12%, causing 1.4 million deaths.2 With the…

Continue Reading Factors influencing multidrug-resistant tuberculosis | IDR

PER1 as a Tumor Suppressor Attenuates Breast Cancer

Introduction Breast cancer is one of the most common malignancies in women, with a high mortality rate around the world.1,2 Although multidisciplinary therapeutic strategies, including surgical resection, chemoradiotherapy, endocrine and anti-HER2 therapy, have made substantial progress over the past decade, there are still a considerable proportion of breast cancer patients…

Continue Reading PER1 as a Tumor Suppressor Attenuates Breast Cancer

LncRNA MIAT services as a noninvasive biomarker

Introduction BC is the most common cancer among women that is responsible for the most of the cancer-related death in worldwide.1 The occurrence of BC accounts for 7–8% of the entire number of malignant tumors.2 Accumulating evidence have shown that immunoreaction plays an important role in oncogenesis and progression.3,4 However,…

Continue Reading LncRNA MIAT services as a noninvasive biomarker

The translatome of neuronal cell bodies, dendrites, and axons

Significance Proteins are the key drivers of neuronal synaptic function. The regulation of gene expression is important for the formation and modification of synapses throughout the lifespan. The complexity of dendrites and axons imposes unique challenges for protein supply at remote locations. The discovery of messenger RNAs (mRNAs) and ribosomes…

Continue Reading The translatome of neuronal cell bodies, dendrites, and axons

Population structure, biogeography and transmissibility of Mycobacterium tuberculosis

Detailed population structure of L1–4 and a hierarchical sub-lineage naming system We assembled a high-quality data set of whole genomes, antibiotic resistance phenotypes, and geographic sites of isolation for 9584 clinical Mtb samples (“Methods” section and Supplementary Data 1). Of the total, 4939 (52%) were pan-susceptible, i.e., susceptible to at least…

Continue Reading Population structure, biogeography and transmissibility of Mycobacterium tuberculosis

Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota

Probiotic intake commonly altered the genetic composition of gut microbial residents To comprehensively understand the adaptive mutations in the resident gut microbiota due to probiotic intake, we first collected and curated publicly available metagenomic studies related to probiotics with the following criteria. (1) The study has a longitudinal design, which…

Continue Reading Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota

Comparison of sequencing data processing pipelines and application to underrepresented African human populations | BMC Bioinformatics

Literature survey We reviewed the processing pipelines of 29 HTS studies, 23 of which focus on human populations and six on other mammals (listed in Table 1). Table 1 List of studies included in the literature survey We summarized the information for some processing steps in Table 2 (see Additional…

Continue Reading Comparison of sequencing data processing pipelines and application to underrepresented African human populations | BMC Bioinformatics

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

Continue Reading Comparative cellular analysis of motor cortex in human, marmoset and mouse

Comparing two RNA-seq data sets mouse and human

Comparing two RNA-seq data sets mouse and human 0 Hi I have a question. We have two RNA-Seq data sets one from mouse and one from human for our gene modification, and we wanted to know how similar they are from each other. I know i can convert the mouse…

Continue Reading Comparing two RNA-seq data sets mouse and human

Microsatellites bioinformatics analysis for population genetics – Freelance Job in Physical Sciences – Less than 30 hrs/week – Less than 1 month

Looking for a bioinformatician biologist for data analysis as soon as possible with Expertise in using the below software 1. FSTAT v2.9.3.2 (Goudet, 1995): For allelic richness (AR) (with the rarefaction method to correct for differences in sample size) 2. BOTTLENECK v1.2.02 (Cornuet & Luikart, 1996; Piry et al., 1999)…

Continue Reading Microsatellites bioinformatics analysis for population genetics – Freelance Job in Physical Sciences – Less than 30 hrs/week – Less than 1 month

Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

Continue Reading Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

Bioconductor – ALDEx2

DOI: 10.18129/B9.bioc.ALDEx2     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ALDEx2. Analysis Of Differential Abundance Taking Sample Variation Into Account Bioconductor version: 3.9 A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard…

Continue Reading Bioconductor – ALDEx2

Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

Continue Reading Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

An epigenetic basis of inbreeding depression in maize

INTRODUCTION Charles R. Darwin documented inbreeding depression as growth disadvantages from self-fertilization compared to outcrossing in many plants (1). Prevailing hypotheses suggest that inbreeding depression results from the exposure of deleterious recessive alleles and/or loss of overdominant alleles due to increased homozygosity (2, 3) or reduced recombination frequency in some…

Continue Reading An epigenetic basis of inbreeding depression in maize

Bioconductor – unifiedWMWqPCR

DOI: 10.18129/B9.bioc.unifiedWMWqPCR     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see unifiedWMWqPCR. Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data Bioconductor version: 3.11 This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing…

Continue Reading Bioconductor – unifiedWMWqPCR

Integrated bioinformatics analysis to identify abnormal CC

Introduction In recent years, the morbidity and mortality of colon cancer have increased rapidly, both being ranked fourth worldwide. Although surgery-based comprehensive treatments improve the prognosis of colon cancer, because of the lack of available means for early diagnosis, the mortality level remains high for patients with advanced-stage cancer. The…

Continue Reading Integrated bioinformatics analysis to identify abnormal CC

Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer

Significance During the aging process, senescent cells secrete inflammatory factors, causing various age-related pathologies. Thus, controlling the senescence-associated secretory phenotype (SASP) can tremendously benefit human health. Although SASP seems to be induced by the alteration of chromosomal organization, its underlying mechanism remains unclear. Here, it has been revealed that noncoding…

Continue Reading Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer

How to adjust p value after Wilcoxon rank sum test?

How to adjust p value after Wilcoxon rank sum test? 0 Can you please help me figure out how the adjusted p-values were obtained in the attached figure. Did they perform Wilcoxon rank sum test and then divided the resultant pvalue with the total number of genes tested? The figure…

Continue Reading How to adjust p value after Wilcoxon rank sum test?