Venn diagram analysis overestimates the extent of circadian rhythm reprogramming

ABSTRACTDue to the limited sensitivities of stool-based microscopy and/or culture techniques forStrongyloides stercoralis, the detection of antibodies to this intestinal nematode is relied upon as a surrogate for determining exposure status or making a diagnosis ofS. stercoralisinfection. Here, we evaluated three immunoassays, including the recently released InBios Strongy Detect IgG enzyme-linked immunosorbent assay (ELISA) (InBios International, Inc., Seattle, WA), the SciMedxStrongyloidesserology microwell ELISA (SciMedx Corporation, Denville, NJ), and the luciferase immunoprecipitation system (LIPS) assay performed at the National Institutes of Health (NIH), for their detection of IgG antibodies toS. stercoralis. A total of 101 retrospective serum samples, previously submitted for routineS. stercoralisantibody detection using the SciMedx assay, were also evaluated by the InBios and LIPS assays. The qualitative results from each assay were compared using a Venn diagram analysis, to the consensus result among the three assays, and each ELISA was also evaluated using the LIPS assay as the reference standard. By Venn diagram analysis, 65% (66/101) of the samples demonstrated perfect agreement by all three assays. Also, the numbers of samples considered positive or negative by a single method were similar. Compared to the consensus result, the overall percent agreement of the InBios, SciMedx, and LIPS assays were comparable at 87.1%, 84.2%, and 89.1%, respectively. Finally, the two ELISAs performed analogously but demonstrated only moderate agreement (kappa coefficient for the two assays, 0.53) with the LIPS assay. Collectively, while the two commercially available ELISAs perform equivalently, neither should be used independently of clinical evaluation to diagnose strongyloidiasis.

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Studies overestimate the extent of circadian rhythm reprogramming in response to dietary and genetic changes

10.1101/2020.12.18.423465 ◽

2020 ◽

Author(s):

Anne Pelikan ◽

Hanspeter Herzel ◽

Achim Kramer ◽

Bharath Ananthasubramaniam

Keyword(s):

R Package ◽

Biological Data ◽

Venn Diagram ◽

Multiple Time ◽

Genetic Changes ◽

Physiological Processes ◽

Multiple Time Points ◽

Gain Loss ◽

Diagram Analysis

AbstractThe circadian clock modulates key physiological processes in many organisms. This widespread role of circadian rhythms is typically characterized at the molecular level by profiling the transcriptome at multiple time points. Subsequent analysis identifies transcripts with altered rhythms between control and perturbed conditions, i.e., are differentially rhythmic (DiffR). Commonly, Venn Diagram analysis (VDA) compares lists of rhythmic transcripts to catalog transcripts with rhythms in both conditions or have gained or lost rhythms. However, unavoidable errors in the rhythmicity detection propagate to the final DiffR classification resulting in overestimated DiffR. We show using artificial experiments constructed from biological data that VDA indeed produces excessive false DiffR hits both in the presence and absence of true DiffR transcripts. We present a hypothesis testing and a model selection approaches in an R-package compareRhythms that instead compare circadian amplitude and phase of transcripts between the two conditions. These methods identify transcripts with ‘gain’, ‘loss’, ‘change’ or have the ‘same’ rhythms; the third category is missed by VDA. We reanalyzed three studies on the interplay between metabolism and the clock in the mouse liver that used VDA. We found not only fewer DiffR transcripts than originally reported, but VDA overlooked many relevant DiffR transcripts. Our analyses confirmed some and contradicted other conclusions in the original studies and also generated novel hypotheses. Our insights also generalize easily to studies using other -omics technologies. We trust that avoiding Venn Diagrams and using our R-package will contribute to improved reproducibility in chronobiology.

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iTRAQ-Based Proteomic Profiling of PLC-Mediated Expression of 20E-Induced Protein in Apolygus lucorum (Meyer-Dür)

10.1101/2020.10.15.341115 ◽

2020 ◽

Author(s):

Yong-An Tan ◽

Xu-Dong Zhao ◽

Jing Zhao ◽

Qin-Qin Ji ◽

Liu-Bin Xiao ◽

...

Keyword(s):

Enrichment Analysis ◽

Venn Diagram ◽

Bt Cotton ◽

Proteomic Profiling ◽

Absolute Quantitation ◽

Apolygus Lucorum ◽

Associated Proteins ◽

Isobaric Tag ◽

First Time ◽

Diagram Analysis

AbstractThe polyphagous pest Apolygus lucorum has become the dominant insect in Bacillus thuringiensis (Bt) cotton fields. The hormone 20-hydroxyecdysone (20E) regulates multiple events in insect development and physiology. 20E responses are controlled by pathways triggered by phospholipase C (PLC)-associated proteins. However, 20E-modulated genes whose expression is affected by PLC remain unknown. Here, isobaric tag for relative and absolute quantitation (iTRAQ) and immunoblot were carried out for comparing differentially expressed proteins (DEPs) in A. lucorum in response to 20E and the PLC inhibitor U73122, respectively. Totally 1624 DEPs were, respectively, found in the 20E/control, U73122/control, and 20E+U73122/control groups. Venn diagram analysis further revealed 8 DEPs that were shared among the three groups. Immunoblot validated these findings, which corroborated and highlighted the reliability of proteomics. KEGG enrichment analysis showed that the DEPs were included in diverse signaling pathways. The largest portion of DEPs among the three groups were categorized in metabolic pathways. In addition, DEPs among the three groups were also found to regulate the Ras-MAPK and PI3K-AKT pathways. This is the first time that iTRAQ was carried out to assess proteome alteration in A. lucorum nymphs in response to 20E and a PLC inhibitor. These findings provide novel insights into protein expression in A. lucorum in response to 20E, and a more comprehensive understanding of the function of PLC in 20E signal transduction.

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Representation of the temporal raphe within the optic tract of the cat

Visual Neuroscience ◽

10.1017/s0952523800001176 ◽

1989 ◽

Vol 2 (3) ◽

pp. 255-267 ◽

Cited By ~ 8

Author(s):

T. Fitzgibbon ◽

W. Burke

Keyword(s):

Optic Disc ◽

Ganglion Cells ◽

Optic Tract ◽

Cell Labeling ◽

Venn Diagram ◽

Retinal Ganglion ◽

Retinal Topography ◽

Area Centralis ◽

Diagram Analysis ◽

Lateral Tract

AbstractThe retinal topography of the cat's optic tract was determined by means of injections of the enzyme horseradish peroxidase (HRP) into the tract. This analysis was accomplished by the subtraction of all HRP injection sites not labeling a defined retinal area from those injection sites which resulted in ganglion cell labeling (Venn diagram analysis). Using this method, the following correspondences were demonstrated for the ipsilateral and contralateral projections: superior retina represented in medial optic tract; inferior retina in lateral tract; and area centralis in a dorsocentral location (which was part of a larger area representing the visual streak). The temporal raphe was represented in the ipsilateral tract as a band curving from the area centralis region toward the dorsomedial border of the tract. Contralateral fibers from a region superior to the optic disc were found to be displaced with respect to the general retinal representation in the optic tract and this appeared to be related to retinal development. The ratio of contralateral to ipsilateral fibers was determined and found to be nonuniform within the tract.Injection of HRP into the optic tract of the cat also allowed the axons from labeled retinal ganglion cells to be traced within the retina and optic disc. Axons from ganglion cells lying temporal to the raphe curve around the area centralis enter the optic disc on the lateral and inferior aspects. Ganglion cells lying nasal to the raphe send their axons more directly to enter the optic disc on its superior aspect. A schema is proposed whereby the retina is mapped onto the optic tract.

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Metabolite Profiling of Different Sweet sorghum cultivars Seeds

10.21203/rs.2.10683/v1 ◽

2019 ◽

Author(s):

Yaxing Zhou ◽

Zhenguo Wang ◽

Yan Li ◽

Zhigang Li ◽

Hui Liu ◽

...

Keyword(s):

Sweet Sorghum ◽

Principal Component ◽

Venn Diagram ◽

Seed Color ◽

Benzoic Acid Derivatives ◽

Orthogonal Signal Correction ◽

Signal Correction ◽

Comparison Groups ◽

Different Color ◽

Diagram Analysis

Abstract Background Sorghum bicolor is one of the most important cereal crops in the world and is widely grown in arid or semi-arid areas. Results This study focused on the metabolic Diversity of three Sweet sorghum cultivars with white, red, and purple seeds to elucidate the factors responsible for the differences in Seed color. We found 651 metabolites were divided into 24 categories including Lipids_Fatty acids, Lipids_Glycerolipids, Flavonoid, Benzoic acid derivatives, Anthocyanins, Nucleotide and its derivates, etc. Through clustering analysis, principal component analysis (PCA), and orthogonal signal correction and partial least squares-discriminant analysis (OPLS-DA), different samples were clearly separated. It shows that contained metabolites of three groups are quite different. There are 217 significantly different metabolites between Z27 and HC4 (106 down-regulated, 111up-regulated), 240 between Z6 and HC4 (58 down-regulated, 182 up-regulated), 199 between Z6 and Z27 (54 down-regulated, 135 up-regulated). Venn diagram analysis indicated that 45 the differential metabolites were common to all three comparison groups. Conclusions This study provides new insights into the differences of metabolites between different color seeds and provides theoretical basis for the sufficient utilization of Sweet sorghum cultivars.

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16S rRNA–Based Analysis Reveals Differences in the Bacterial Community Present in Tissues of Choromytilus chorus (Mytilidae, Bivalvia) Grown in an Estuary and a Bay in Southern Chile

Diversity ◽

10.3390/d13050209 ◽

2021 ◽

Vol 13 (5) ◽

pp. 209

Author(s):

Tamara Valenzuela ◽

Joaquin I. Riling ◽

Giovanni Larama ◽

Jacquelinne J. Acuña ◽

Marco Campos ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

Illumina Miseq ◽

16S Rrna Genes ◽

Rrna Genes ◽

Venn Diagram ◽

Linear Discriminant ◽

Operational Taxonomic Units ◽

Marine Bivalves ◽

Diagram Analysis

Microbiota associated with bivalves have drawn considerable attention because studies have suggested their relevance to the fitness and growth of marine bivalves. Although the mussel Choromytilus chorus is a valuable resource for Chilean aquaculture and fisheries, its microbiota is still unknown. In this study, the composition and predicted functions of the bacterial community in tissues of C. chorus specimens grown in an estuary (Nehuentue) and a bay (Hueihue) were investigated. Using 16S rRNA genes as targets, the bacterial abundance in tissues was estimated by quantitative PCR and sequenced via Illumina MiSeq. The abundances of bacteria ranged from 103 to 105 copies of 16S rRNA genes g−1 tissue. In the Nehuentue estuary, the bacterial communities in the tissues were dominated by the Tenericutes phylum, whereas the Tenericutes and Proteobacteria phyla dominated in mussels from Hueihue Bay. Higher numbers of operational taxonomic units (OTUs) were observed in tissues from the Nehuentue Estuary than in those from Hueihue Bay. Differences in bacterial community compositions in tissues between both locations were confirmed by nonmetric multidimensional scaling (nMDS) and Venn diagram analysis. In addition, linear discriminant analysis effect size (LEfSe) revealed that the Mollicutes class and Actynomycetales order were key phylotypes in tissues from the Nehuentue Estuary and Hueihue Bay, respectively. Our analysis also predicted a high abundance of sequences assigned to heterotrophy; however, relatively high functional diversity was also found in tissues from Hueihue Bay. This work represents our first attempt to elucidate the C. chorus microbiota in contrasting Chilean aquatic environments.

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Antibody array-based proteomic screening of novel biomarkers in malignant biliary stricture

Cancer Biomarkers ◽

10.3233/cbm-210095 ◽

2021 ◽

pp. 1-10

Author(s):

Wen-Hao Qin ◽

Jun-Teng Liu ◽

Shu-Ping Wang ◽

Zhi-Shi Yang ◽

Kun-Ke Wang ◽

...

Keyword(s):

Biliary Stricture ◽

Venn Diagram ◽

Antibody Array ◽

Human Antibody ◽

Lipocalin 2 ◽

Biliary Strictures ◽

Diagnostic Challenge ◽

Benign Biliary Strictures ◽

Novel Biomarkers ◽

Diagram Analysis

BACKGROUND: Distinguishing between benign and malignant bile duct strictures has long been a diagnostic challenge in clinical practice. OBJECTIVE: This study aimed to discover novel biomarkers in bile to improve the diagnostic accuracy of malignant biliary strictures. METHODS: Bile samples were collected from 6 patients with malignant or benign biliary stricture, respectively. Protein profiles of the bile were analyzed with a semi-quantitative human antibody array of 440 proteins. Then the differential expressed proteins were screened by Venn diagram analysis. Following this, the accuracy of these potential biomarkers for discriminating between malignant and non-malignant biliary strictures was validated in a larger (n= 40) group of patients using lasso analysis. Results: Twenty proteins were found differentially expressed in malignant versus benign biliary strictures, 6 of which were identified by Venn diagram analysis to be up-regulated regardless of the location of biliary strictures. Among the 6 biomarkers, bile lipocalin-2, P-cadherin, and adipsin showed better diagnostic utility than that of bile CA19-9. Lasso analysis identified that lipocalin-2, P-cadherin and CA19-9 as a group of makers best distinguished malignant from benign strictures. CONCLUSIONS: Lipocalin-2 and P-cadherin measurements in bile could be clinically useful for the detection of malignant biliary strictures.

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Screening for Key Pathways Associated with the Development of Osteoporosis by Bioinformatics Analysis

BioMed Research International ◽

10.1155/2017/8589347 ◽

2017 ◽

Vol 2017 ◽

pp. 1-8

Author(s):

Yanqing Liu ◽

Yueqiu Wang ◽

Yanxia Zhang ◽

Zhiyong Liu ◽

Hongfei Xiang ◽

...

Keyword(s):

Rho Gtpases ◽

Bioinformatics Analysis ◽

Venn Diagram ◽

Mitotic Metaphase ◽

Profile Data ◽

Functional Interaction ◽

Pathway Enrichment ◽

Comparison Groups ◽

Key Pathways ◽

Diagram Analysis

Objectives.We aimed to find the key pathways associated with the development of osteoporosis.Methods.We downloaded expression profile data of GSE35959 and analyzed the differentially expressed genes (DEGs) in 3 comparison groups (old_op versus middle, old_op versus old, and old_op versus senescent). KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses were carried out. Besides, Venn diagram analysis and gene functional interaction (FI) network analysis were performed.Results.Totally 520 DEGs, 966 DEGs, and 709 DEGs were obtained in old_op versus middle, old_op versus old, and old_op versus senescent groups, respectively. Lysosome pathway was the significantly enriched pathways enriched by intersection genes. The pathways enriched by subnetwork modules suggested that mitotic metaphase and anaphase and signaling by Rho GTPases in module 1 had more proteins from module.Conclusions.Lysosome pathway, mitotic metaphase and anaphase, and signaling by Rho GTPases may be involved in the development of osteoporosis. Furthermore, Rho GTPases may regulate the balance of bone resorption and bone formation via controlling osteoclast and osteoblast. These 3 pathways may be regarded as the treatment targets for osteoporosis.

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Heat and Hypoxia Exposure Mediates Circadian Rhythms Response via Methylation Modification in Apostichopus japonicas

Frontiers in Marine Science ◽

10.3389/fmars.2021.721465 ◽

2021 ◽

Vol 8 ◽

Author(s):

Jiong Wu ◽

Weiwei Zhang ◽

Chenghua Li

Keyword(s):

Dna Methylation ◽

Circadian Rhythm ◽

Cpg Island ◽

Apostichopus Japonicus ◽

Combined Treatment ◽

Cpg Islands ◽

Venn Diagram ◽

Hypoxia Exposure ◽

Rate Limiting Step ◽

Genome Methylation

As global warming progresses, heat and hypoxia are gradually becoming important factors threatening the survival, reproduction, and development of marine organisms. To determine the effect of heat and hypoxia on Apostichopus japonicus, whole genome methylation of the respiratory tree was determined under heat, hypoxia, and heat-hypoxia conditions [designed as heat stress treatment (HT), hypoxia treatment (LO), and heat-hypoxia combined treatment (HL) groups]. The number of differentially methylated regions (DMRs) under three treatments was determined based on the Venn diagram. The network of the DMRs associated with promoters that were co-existed under the three conditions showed that circadian rhythm was involved based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Circadian rhythm-related genes, CRY1a, CRY1b, CLC, and TIM, decreased in LO and HL groups, while CRY1a, CRY1b, and BMAL1 increased in the HT group. Bisulfite sequencing PCR (BSP) showed that the methylation levels of CpG island regions in the promoters of CRY1a and CRY1b were upregulated in HT, LO, and HL groups, leading to the decreased promoter activity of CRY1a and CRY1b. RNAi of CRY1a and CRY1b led to increased enzyme activities of two energy-related enzymes, pyruvate kinase (PK) catalyzing the rate-limiting step in glycolysis, and ATPase hydrolyzing ATP to ADP, which were also increased under the three tested conditions. Thus, it was concluded that A. japonicus may respond to the heat, hypoxia, and heat-hypoxia stresses via the DNA methylation of heat, hypoxia, and heat-hypoxia stresses via the DNA methylation of CpG islands of circadian rhythm-related genes, which increased the activity of energy-related enzymes.

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A circadian rhythm in adult idiopathic epistaxis?

Clinical Otolaryngology ◽

10.1046/j.1365-2273.1998.0138c.x ◽

1998 ◽

Vol 23 (3) ◽

pp. 280-280 ◽

Cited By ~ 2

Author(s):

Mehanna ◽

Robinson ◽

Gatehouse ◽

Mcgarry

Keyword(s):

Circadian Rhythm ◽

Idiopathic Epistaxis

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