Category: CNA

Genome-Wide cfDNA Analysis Detects Therapy Response in B-Cell Lymphoma – Hematology

Image: The Bio-Rad QX200 Droplet Digital PCR (ddPCR) reader (Photo courtesy of University of California Santa Barbara) Diffuse large B-cell lymphoma (DLBCL) is the most common, aggressive type of non-Hodgkin lymphoma. Although 50% to 60% of individuals achieve cure with chemoimmunotherapy, outcomes are poor for relapsed/refractory disease. Chimeric antigen receptor…

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Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data

Somatic point mutation calling suggests Mutect2 is best for subclonal variants We applied four somatic variant callers (Mutect211, Strelka212, VarScan213 and Lancet14) to a highly mutated tumour dataset (S3R3) at 100% tumour purity across all sequencing depths. Runtimes differed substantially between methods, with Strelka2 being fastest and Mutect2 taking longest…

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Copy Number to Log2_ratio for autosomal

Copy Number to Log2_ratio for autosomal 0 Hi, I want to transform some ASCAT data into log2_r values. The file contains at total copy number column. I would then take fold ratio of the total copy number versus the natural ploidy, correct? Can I assume the natural ploidy for all…

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AKIRIN2 controls the nuclear import of proteasomes in vertebrates

1. Johnston, L. A., Prober, D. A., Edgar, B. A., Eisenman, R. N. & Gallant, P. Drosophila myc regulates cellular growth during development. Cell 98, 779–790 (1999). CAS  PubMed  Article  Google Scholar  2. Sabo, A. et al. Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis. Nature 511,…

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Relation between copy number log ratio and copy number

Relation between copy number log ratio and copy number 0 Currently, I’m researching to get the minor, major copy number in tumor samples, so that I can use them in Pyclone. I have tried CNV caller such as PureCN, Sequenza and TitanCNA so far. The caller calculates the most optimal…

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Worker-dependent gut symbiosis in an ant

1. Lundberg JO, Weitzberg E, Cole JA, Benjamin N. Nitrate, bacteria and human health. Nat Rev Microbiol. 2004;2:593–602. CAS  PubMed  Article  PubMed Central  Google Scholar  2. Bulgarelli D, Schlaeppi K, Spaepen S, Van Themaat EVL, Schulze-Lefert P. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol….

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Get Allele specific copy number regions from WGS data using ASCAT?

Get Allele specific copy number regions from WGS data using ASCAT? 0 Hi, I have some paired samples(normal vs. tumour) and want to do allele specific CNA analysis. can you help me to check if I use the right pipeline? I use bcftools mpileup and call to call snp from…

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States Are Toughening Up on Genetic Privacy

If you’ve ever spit into a plastic tube or swabbed your cheek and mailed your saliva away to learn about your ancestry or health risks, you might have assumed that the company analyzing your DNA is legally required to keep your genetic data private. But you’d be wrong. The Health…

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Identification of Hub mRNAs and lncRNAs in Atrial Fibrillation Using Weighted Co-expression Network Analysis With RNA-Seq Data

This article was originally published here Front Cell Dev Biol. 2021 Oct 4;9:722671. doi: 10.3389/fcell.2021.722671. eCollection 2021. ABSTRACT Atrial fibrillation (AF)/paroxysmal AF (PAF) is the main cause of cardiogenic embolism. In recent years, the progression from paroxysmal AF to persistent AF has attracted more and more attention. However, the molecular…

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Become a Bioinformatics Scientist: Step-by-Step Career Guide

Bibliography: Best Accredited Colleges / Become a Bioinformatics Scientist: Step-by-Step Career Guide. (2021, Oct 20 of publication). Retrieved from bestaccreditedcolleges.org/articles/become-a-bioinformatics-scientist-step-by-step-career-guide.html Bibliography: Best Accredited Colleges / Become a Bioinformatics Scientist: Step-by-Step Career Guide. (2021, Oct 20 of publication). Retrieved from bestaccreditedcolleges.org/articles/become-a-bioinformatics-scientist-step-by-step-career-guide.html Copy to clipboard In Text: (Become a Bioinformatics Scientist: Step-by-Step…

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Is it possible to programmatically download the tables containing mutations, structural variants and CNAs shown in the summary section of an specific patient?

cBioPortal: Is it possible to programmatically download the tables containing mutations, structural variants and CNAs shown in the summary section of an specific patient? 0 Hello everyone! I’m currently working with the TCGA-BRCA dataset, using the data provided by both GDC Portal and cBioPortal. There is some processed data displayed…

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Severe trauma and burns accompanied by sepsis

Introduction Trauma accounts for approximately 10% of deaths and 16% of disabilities worldwide.1 Billions of dollars have been spent on research into new biological therapeutics for severe injuries, as well as post-traumatic sepsis and septic shock.2 Burn injuries cause unpredictable trauma and sepsis is a complication associated with high morbidity…

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Opposite Signed Genes in WGCNA Signed Consensus Analysis

Hello, I was wondering if anyone could tell me how it would be possible to have genes that have negative correlations (as determined by kME values) with a module in a signed WGCNA analysis. My understanding is that, by definition, all the genes in a module should have a positive…

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how to get ride of duplicated genes when we also have duplicated Ensemble ID in the expression profile?

how to get ride of duplicated genes when we also have duplicated Ensemble ID in the expression profile? 0 Hi all, I have a mouse expression profile that is annotated with gene symbols and many of them are duplicated. I usually use collapseRows function with maxMean method from WGCNA package…

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Study Modules significance (or Modules Preservation) in ONE network

Study Modules significance (or Modules Preservation) in ONE network 1 I am studying only one co-expression network utilizing WGCNA. I would like to validate that the modules identified by WGCNA are significantly above randomly generated modules. 1. What would be the best way to do it? 2. Is there a…

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Identification of Hub Genes Associated With Clear Cell Renal Cell Carcinoma by Integrated Bioinformatics Analysis

This article was originally published here Front Oncol. 2021 Sep 30;11:726655. doi: 10.3389/fonc.2021.726655. eCollection 2021. ABSTRACT BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is a common genitourinary cancer type with a high mortality rate. Due to a diverse range of biochemical alterations and a high level of tumor heterogeneity, it…

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The Profile and Function of Gut Microbiota in Diabetic Nephropathy

Introduction Diabetic nephropathy (DN) is characterized by kidney function loss caused by diabetes mellitus.1 Almost one-third of patients with diabetes have DN, and the prevalence of DN is increasing worldwide.2 DN is one of the most important factors of chronic kidney disease and end-stage renal disease (ESRD). The signs and…

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Following the Trace of HVS II Mitochondrial Region Within the Nine Iranian Ethnic Groups Based on Genetic Population Analysis

Akbari MT, Izadi P, Izadyar M, Kyriacou K, Kleanthous M (2008) Molecular basis of thalassemia intermedia in Iran. Hemoglobin 32:462–470 CAS  Article  Google Scholar  Al-Allawi NA, Jubrael JM, Hughson M (2006) Molecular characterization of β-thalassemia in the Dohuk region of Iraq. Hemoglobin 30:479–486 CAS  Article  Google Scholar  Alibakhshi R, Kianishirazi…

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KEGG ENZYME: 1.4.1.4

Entry EC 1.4.1.4                  Enzyme                                  Name glutamate dehydrogenase (NADP+);glutamic dehydrogenase;dehydrogenase, glutamate (nicotinamide adenine dinucleotide (phosphate));glutamic acid dehydrogenase;L-glutamate dehydrogenase;L-glutamic acid dehydrogenase;NAD(P)+-glutamate dehydrogenase;NAD(P)H-dependent glutamate dehydrogenase;glutamate dehydrogenase (NADP+) Class Oxidoreductases;Acting on the CH-NH2 group of donors;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname L-glutamate:NADP+ oxidoreductase (deaminating) Reaction(IUBMB) L-glutamate + H2O + NADP+ = 2-oxoglutarate + NH3…

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Lipid biomarkers: molecular tools for illuminating the history of microbial life

1. Berner, E. K. & Berner, R. A. Global Environment: Water, Air, and Geochemical Cycles (Princeton Univ. Press, 2012). 2. Cavosie, A. J., Valley, J. W. & Wilde, S. A. The oldest terrestrial mineral record: a review of 4400 to 4000 Ma detrital zircons from Jack Hills, Western Australia. Dev….

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The population genomic structure of green turtles (Chelonia mydas) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial

Alfaro-Nunez A, Bertelsen MF, Bojesen AM, Rasmussen I, Zepeda-Mendoza L, Olsen MT et al. (2014) Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles. BMC Evol Biol 14:206 PubMed  PubMed Central  Article  Google Scholar  Ali OA, O’Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C et al….

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Importing WGCNA edge and node files into Cytoscape

I’ve used the WGCNA packages (horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/) to generate edge and node files for use in Cytoscape. cyt = exportNetworkToCytoscape(modTOM, edgeFile = file.path(“./environment”, paste(label, “_CytoscapeInput-edges-“, paste(modules, collapse=”-“), “.txt”, sep=””)), nodeFile = file.path(“./environment”, paste(label, “_CytoscapeInput-nodes-“, paste(modules, collapse=”-“), “.txt”, sep=””)), weighted = TRUE, threshold = 0.02, nodeNames = modProbes, altNodeNames = modGenes, nodeAttr…

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Genetic Factors Affecting Precision Pain Medicine

Introduction The overarching definition of precision pain medicine is that diagnosis and treatment can be customized to an individual’s specific risk profile.1,2 At its most basic, the ideology is based on using all available patient-level data to target therapies for that individual with regard to prediction, prevention, diagnosis, and treatment…

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Caris Life Sciences and ESSA Pharma Announce Liquid Biopsy Profiling Collaboration

IRVING, Texas, and HOUSTON, and VANCOUVER, BC, Oct. 7, 2021 /PRNewswire/ — Caris Life Sciences®, a molecular science company developing and delivering technologies to revolutionize healthcare, and ESSA Pharma Inc. (Nasdaq: EPIX) (“ESSA”), a clinical-stage pharmaceutical company focused on developing novel therapies for the treatment of prostate cancer, announced today…

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Combining different data types into a single matrix for WGCNA using DESeq2 normalization

Combining different data types into a single matrix for WGCNA using DESeq2 normalization 0 Hi, I have two different RNA-seq datasets for the sample set of samples, generated using mRNA-seq and smallRNA-seq. The goal here is to identify a set of coding-genes and smallRNAs (no known function/targets) that act together….

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WGCNA error during network construction

I am performing WGCNA analysis on my RNAseq dataset and getting this error message: >net = blockwiseModules(expression, power = 6, + TOMType = “unsigned”, minModuleSize = 30, + reassignThreshold = 0, mergeCutHeight = 0.25, + numericLabels = TRUE, pamRespectsDendro = FALSE, + saveTOMs = TRUE, + saveTOMFileBase = “SW_TOM”, +…

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KEGG ENZYME: 6.3.2.6

Entry EC 6.3.2.6                  Enzyme                                  Name phosphoribosylaminoimidazolesuccinocarboxamide synthase;phosphoribosylaminoimidazole-succinocarboxamide synthetase;PurC;SAICAR synthetase;4-(N-succinocarboxamide)-5-aminoimidazole synthetase;4-[(N-succinylamino)carbonyl]-5-aminoimidazole ribonucleotide synthetase;SAICARs;phosphoribosylaminoimidazolesuccinocarboxamide synthetase;5-aminoimidazole-4-N-succinocarboxamide ribonucleotide synthetase Class Ligases;Forming carbon-nitrogen bonds;Acid-D-amino-acid ligases (peptide synthases)BRITE hierarchy Sysname 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate:L-aspartate ligase (ADP-forming) Reaction(IUBMB) ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate [RN:R04591] Reaction(KEGG) Substrate ATP [CPD:C00002]; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate [CPD:C04751]; L-aspartate [CPD:C00049] Product ADP [CPD:C00008]; phosphate…

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Heatmap for GISTIC2.0

Heatmap for GISTIC2.0 1 Hi there, In the output of GISTIC2.0 algorithm for copy number analysis, there is a generated heatmap Segmented Copy Number (raw_copy_number.pdf and raw_copy_number.png). The png file is shown as the following: This file is a heat map image of the segmented copy number profiles in the…

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Mutational profile of the dystrophin gene

Introduction Duchenne Muscular Dystrophy (DMD-OMIM #310200) and Becker Muscular Dystrophy (BMD-OMIM #300376), are the most common hereditary muscular dystrophies around the world.1 DMD and BMD occur with a frequency of 1/3.300 and 1/6.000 newborn males, respectively.2 These dystrophinopathies are caused by alterations in the DMD gene and have an X-linked…

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PCA result and batch effect?

PCA result and batch effect? 0 Hello, I am processing a dataframe that consists of about 55000 genes(TPM values,no access to raw data) and 400 samples. After removing the zero variance genes, I am performing a PCA on the samples trying to detect outliers. I have noticed that there are…

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Murrieta Genomics Spinout simplSEQ to Present Novel Multi-Omic Technology at Sequencing, Finishing and Analysis in the Future Meeting | News

MURRIETA, Calif., Sept. 28, 2021 /PRNewswire-PRWeb/ — Murrieta Genomics, the launch pad for genomic sequencing startups, is pleased to announce that simplSEQ, an incubator company and subsidiary, will be presenting a novel and proprietary approach to sample preparation that will enable researchers to analyze nucleic acids and all other molecules…

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Murrieta Genomics Spinout simplSEQ to Present Novel Multi-Omic Technology at Sequencing, Finishing and Analysis in the Future Meeting

Novel Technology Enables Multiple Analyses from Single Plasma Sample MURRIETA, Calif., Sept. 28, 2021 /PRNewswire-PRWeb/ — Murrieta Genomics, the launch pad for genomic sequencing startups, is pleased to announce that simplSEQ, an incubator company and subsidiary, will be presenting a novel and proprietary approach to sample preparation that will enable…

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Plot genes derived from time course experiment as line graph

Plot genes derived from time course experiment as line graph 0 Hi! I would like to plot the log2FC of 80 genes of a time course experiment (from 0 to 168hrs) as line plot. So originally my dataset has the genes in rows and the log2FC per time point in…

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KEGG ENZYME: 3.6.1.22

Entry EC 3.6.1.22                 Enzyme                                  Name NAD+ diphosphatase;NPY1 (gene name);nudC (gene name);NUDT7 (gene name);nicotinamide adenine dinucleotide pyrophosphatase;NADP pyrophosphatase;NADH pyrophosphatase;NAD+ phosphohydrolase Class Hydrolases;Acting on acid anhydrides;In phosphorus-containing anhydridesBRITE hierarchy Sysname NAD(H) phosphohydrolase Reaction(IUBMB) Reaction(KEGG) Substrate Product Comment This enzyme, described from plants, animals, and bacteria, can act on both reduced and oxidized forms of…

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KEGG ENZYME: 2.6.1.52

Entry EC 2.6.1.52                 Enzyme                                  Name phosphoserine transaminase;PSAT;phosphoserine aminotransferase;3-phosphoserine aminotransferase;hydroxypyruvic phosphate-glutamic transaminase;L-phosphoserine aminotransferase;phosphohydroxypyruvate transaminase;phosphohydroxypyruvic-glutamic transaminase;3-O-phospho-L-serine:2-oxoglutarate aminotransferase;SerC;PdxC;3PHP transaminase Class Transferases;Transferring nitrogenous groups;TransaminasesBRITE hierarchy Sysname O-phospho-L-serine:2-oxoglutarate aminotransferase Reaction(IUBMB) (1) O-phospho-L-serine + 2-oxoglutarate = 3-phosphooxypyruvate + L-glutamate [RN:R04173]; (2) 4-phosphooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate [RN:R05085] Reaction(KEGG) Substrate O-phospho-L-serine [CPD:C01005]; 2-oxoglutarate [CPD:C00026]; 4-phosphooxy-L-threonine [CPD:C06055] Product…

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Extracting The Features From Genbank File

Hi I have a set of the genes (mouse) for which i would like to get the function, tissue specificity and other features. I have obtained a file (.dat) from uniprot which has all such information. but it also has unwanted information. The data seems to be in genbank format….

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Physiological and histopathological effects of electroporation pulse on stomach of rats | BMC Gastroenterology

Animal care and ethics Ninety male Sprague Dawley rats (180–280 g) were purchased and kept at the Experimental Animal Center of Xi’an Jiaotong University. The animals were maintained in standard day and night cycle (12 h light to 12 h dark) and environment temperature (25 ± 2 °C) with free access to food and water. All…

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WGCNA Labeled Heatmap

Hi. I’m trying to create a labelled heatmap of module trait relationships using the following code from the WGCNA tutorial: png(filename = “Module-Trait Relationship.png”, width = 20, height = 30, res=300, unit=”cm”) par(mar = c(6, 8.5, 3, 3)) labeledHeatmap(Matrix = moduleTraitCor, xLabels = names(stressdatTraits), yLabels = names(MEs), ySymbols = names(MEs),…

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Connectivity, diversity, and hybridization between two endemic fish species (Percilia spp.) in a complex temperate landscape

Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229. doi.org/10.1175/1520-0442(1992)0052.0.CO;2 CAS  Article  PubMed  PubMed Central  Google Scholar  Arratia G (1982) A Review of freshwater percoids from South America (Pisces, Osteichthyes, Perciformes, Percichthyidae, and Peciliidae). Abh Senckenb Naturforsch Ges 15:1–52 Google Scholar …

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Shotgun scanning glycomutagenesis: A simple and efficient strategy for constructing and characterizing neoglycoproteins

Glycosylation of asparagine residues is one of the most abundant and structurally complex protein posttranslational modifications (1, 2) and occurs in all domains of life (3). Owing to their relatively large size and hydrophilicity or simply their presence at definite locations, asparagine-linked (N-linked) glycans can significantly alter protein properties including…

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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,…

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WGCNA, what does it mean if no hub genes are identified?

WGCNA, what does it mean if no hub genes are identified? 0 I ran WGCNA for my genes following the tutorials by Horvath and Langfelder (horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/). I’ve obtained my modules and the GS and MM for my list of genes – however I think my situation is a bit odd….

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Why there are same name with different value in my microarray result?

Why there are same name with different value in my microarray result? 0 I have done one color agilent microarray. I am processing my data, but my data showed one miRNA present in more than one place with different value. Could someone please tell me what is the reason for…

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MemVerge Big Memory Technology Speeds Genomic Analytic Processes for Penn State Huck Institutes of the Life Sciences

MemVerge Memory Machine Dramatically Cuts Genome Sequencing Processes for Plant DNA Analytics to Help Develop More Sustainable Plant Products MILPITAS, Calif., Sept. 21, 2021 /PRNewswire/ — MemVerge®, the pioneers of Big Memory software, today announced Memory Machine™ Big Memory virtualization software has been selected by Penn State Huck Institutes of…

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hypothetical protein DAPPUDRAFT_213302, maker-scaffold2255_size18018-snap-gene-0.6 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein DAPPUDRAFT_213302 vs. L. salmonis genes Match: EMLSAG00000000401 (supercontig:LSalAtl2s:LSalAtl2s1063:86108:87342:-1 gene:EMLSAG00000000401 transcript:EMLSAT00000000401 description:”maker-LSalAtl2s1063-snap-gene-0.46″) HSP 1 Score: 149.443 bits (376), Expect = 4.121e-44Identity = 91/196 (46.43%), Postives = 119/196 (60.71%), Query Frame = 0 Query: 14 MDKITDLQVEPLT–NSRFVKPLRLRFKQDGKVKVWDLIQCHASVAVVIFNQTTQKFVFVRQFRPAVYFSALRRAQGDVEPGTQFKGDEIDPKVGITLELCAGIVD-KSKSLIEIAHEEILEETGYDVPMNLIEEIQTFPVGVGVGGENMTLFCAEVTEAMRKGPGGGLAEEGEMIDVIEMGVEETRTLMRAKSVT 206 MDK+ VEPL +SRFV P R+ ++Q+G…

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Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 CAS  PubMed  PubMed Central  Article  Google Scholar  Alexander DH, Shringarpure SS, Novembre J, Lange K (2015) Admixture 1.3 software manual. UCLA Hum Genet Softw Distrib, Los Angeles Google Scholar  Angert AL, Bontrager…

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Primer3 issue with the Sequence_ID

Primer3 issue with the Sequence_ID 0 Hi everyone, I am trying to sign primers for my sequences but I have an error that I do not understand the problem. I made my finputfile.txt and I made the command below: aka@aka:~/Desk/Primer$ /home/aka/primer3/src/primer3_core < input.txt > result.txt input.txt PRIMER_TASK=generic PRIMER_PICK_LEFT_PRIMER=1 PRIMER_PICK_INTERNAL_OLIGO=0 PRIMER_PICK_RIGHT_PRIMER=1…

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probable dimethyladenosine transferase-like, maker-scaffold153_size302544-snap-gene-2.18 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of probable dimethyladenosine transferase-like vs. L. salmonis genes Match: EMLSAG00000006273 (supercontig:LSalAtl2s:LSalAtl2s341:673186:674124:1 gene:EMLSAG00000006273 transcript:EMLSAT00000006273 description:”augustus_masked-LSalAtl2s341-processed-gene-6.3″) HSP 1 Score: 484.567 bits (1246), Expect = 2.083e-174Identity = 227/310 (73.23%), Postives = 259/310 (83.55%), Query Frame = 0 Query: 9 KVRKTGSGMSTVEAAGSGGGGQQGMVFNTGLGQHILKNPLVVQSIIDKAALRSTDVVLEIGPGTGNLTVRALEKCKKLIACEVDPRMVAELQKRVQGTHFQSKLQIMVGDVIKTDLPFFDACVANVPYQISSPLVFKLLLHRPFFRCAVLMFQREFAQRLVAKPGDKLYCRLSINTQLLARVDHVMKVGKGNFRPPPKVESSVVRIEPRNPPPPINFKEWDGLTRVAFVRKNKTLGAAFNQTTVLMMLEKNYRVHLSLADEPVPEKIDIKSIIETVLAEIAFKEKRARSMDIDDFMKLLHAFNAKGIHFV 318 KV+ T + GG+QG+VFNT LGQHILKNP VV…

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Oakland Zoo Invites Public to Relinquish Personal Effects Made From Exotic Animals To Help End the Illegal Wildlife Trade – Oakland News Now

Tag CloudSam Cassidy, Rally at Lake Merritt, Soulbeat Day, Kofi Bonner on future of office work after Pandemic, The Battery SF Club, Oakland Redevelopment Agency, Community Revitalization and Investment Authority , California Capital Investment Group, IFTTT Pro, Bellevue Club Lake Merritt, Michael Birch, Xochi Birch, website, OaklandNewsNow.com, French Open Tennis,…

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Gmod Minecraft Maps | Planet Minecraft Community

Gmod Minecraft Maps | Planet Minecraft Community 1 – 25 of 77 1 – 25 of 77 Top Search Website © 2010 – 2021www.planetminecraft.com //www.planetminecraft.com/css/fonts.css?v=iAIAFChsfiOXhFo1Q2xw8K3yBUtVao3WmHpU39GNnyc7p4lg,//www.planetminecraft.com/css/style.css?v=l1485NRcRIAtDVYEGw7j4TljhDmcctZRkjzSk6dx63pGRCph,//www.planetminecraft.com/css/editor.css?v=I9GbhelPqp_wxFBey8Wwe7xjhAV2rwJSe2-0yLfJMs-KEudg Read more here: Source link

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X amino acid in ensembl

X amino acid in ensembl 2 Hello all, I am working on aligning proteins orthologs from different species. I am using the Ensembl API. Strangely, some protein sequences from non-human species have a lot of X. I wonder what does that mean? In theory, if their genome sequence is know,…

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nyc property sales kaggle

Brilliantly “skewering the disingenuous masquerade of institutional racism” (Publishers Weekly), this dreamlike “smart, funny, and sharp” (Jesmyn Ward), novel shows the work that young Black Americans must do, while living under the … The latter might mean some company purchased a building. Above table shows descriptive statistics for the numeric…

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Gene Expression Analysis Reveals Key Genes and Signalings Associated with the Prognosis of Prostate Cancer

This article was originally published here Comput Math Methods Med. 2021 Aug 28;2021:9946015. doi: 10.1155/2021/9946015. eCollection 2021. ABSTRACT It is urgent to identify novel biomarkers for prostate cancer (PCa) prognosis and to understand the mechanisms regulating the tumorigenesis for PCa treatment. In this study, GSE17951 and TCGA were used to…

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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

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WGCNA

WGCNA 0 0 Entering edit mode 2 hours ago Nithya &utrif; 10 Can any one help to solve this Error?? Installation WGCNA • 15 views ADD COMMENT • link 2 hours ago by Nithya &utrif; 10 Login before adding your answer. Similar Posts Loading Similar Posts Traffic: 1630 users visited…

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Weird PCA plot based on WGCNA results

Weird PCA plot based on WGCNA results 0 Dear all, I used WGCNA to find the associated gene modules with the different subtypes of a given cancer as trait. I obtained multiple modules associated with some of the cancer subtypes as shown in . Next, I plotted PCA to visualize…

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Community detection protocol and failed gene enrichment

My data is a file of about 19000 genes from a 100 patients. I tried to use these data to create a network by using igraph. Firstly, I had all the names of the genes converted to ENTREZID and from the 19000 genes I kept around 14000. Then I had…

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Novel Test Distinguishes Benign From Malignant Lesions in NF1

A novel liquid biopsy test has been shown to distinguish between patients with neurofibromatosis type 1 (NF1) who have benign plexiform neurofibroma (PN) precursor lesions from patients who have malignant peripheral nerve sheath tumors (MPNST), say authors of a multi-institutional cross-sectional study. “Transformation from PN to MPNST is challenging to…

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Apply batch effect with “combat” in wgcna

Apply batch effect with “combat” in wgcna 0 I have 336 samples, with two conditions of fibrosis and normal , and male and female genders , and Chinese, Indian, Malay , Caucasian , Bruneian, and not reported nationalities, I want to apply the batch effect by combat to this study…

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KEGG ENZYME: 1.14.12.17

Entry EC 1.14.12.17               Enzyme                                  Name nitric oxide dioxygenase Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donorBRITE hierarchy Sysname nitric oxide,NAD(P)H:oxygen oxidoreductase Reaction(IUBMB) 2 nitric oxide + 2 O2 + NAD(P)H =…

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Gene expression profiling of contralateral dorsal root gangl

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

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Module preservation analysis using WGCNA

Module preservation analysis using WGCNA 0 Dear Friends, I have the gene expression microarray dataset (about 17000 genes) of about 400 cancer samples with different cancer subtypes (say A, B, C, and D) and about 30 control samples. Here, I used only cancer samples and considered 50% of genes with…

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Single cell DNA sequencing reveals punctuated and gradual clonal evolution in hepatocellular carcinoma

Footnotes Grant support This work is jointly supported by National Natural Science Foundation of China (82173035, 81802813,82030079, 81972656, 81988101, and 81902401), the National Science and Technology Major Project of China (2018ZX10723204), the Michigan Medicine and Peking University Health Science Center Joint Institute for Translational and Clinical Research (BMU2020JI005), Natural Science…

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how to increase modules in WGCNA

how to increase modules in WGCNA 0 Hi, I did wgcna analysis to do the project I used 336 samples for this analysis, but in the end, it gave me 3 modules, about 16,000 genes, 12,000 in one module, 379 in one module, and 212 in another. I think I…

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NAPB Puts a Focus on Breaking Down Barriers

The National Association of Plant Breeders 2021 virtual meeting highlighted the need to reach out and form new collaborations to advance plant breeding for the 21st century. Fabian Leon was born in Bakersfield, Calif., where his parents were migrant farm workers. He grew up in Nicholasville, Kentucky, where his chance at…

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Modification of endoglin-targeting nanoliposomes | IJN

Introduction Today, malignant tumors (cancer) still severely imperil human health and cause millions of global mortality rates.1,2 Deep-seated solid tumors are challenging to cure by most therapeutic tools, mainly blamed on the complex tumor microenvironment (TME).3,4 Adoptive cell therapy (ACT), as one of the effective immunotherapeutic means for cancer treatment,…

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Greenland Sharks Live Hundreds of Years; Can These Sharks Teach Humans How to Live Long?

A fishing expedition 15 years ago off the west coast of Greenland led scientists to discover the world’s oldest vertebrate, Greenland sharks. This species can live at least 250 years. Scientists see lifestyle and genetics as a possible cause, and gene therapy techniques help humans adopt the same longevity.  Danish…

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Regarding finding hub genes using WGCNA

Regarding finding hub genes using WGCNA 1 Dear all, I have got the gene expression microarray dataset (about 17000 genes) of about 400 cancer samples with different cancer subtypes. I considered subtypes as traits (binary traits) and used WGCNA to find the possible modules associated with traits and to identify…

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Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

1. Thompson, J. N. & Pellmyr, O. Evolution of oviposition behavior and host preference in Lepidoptera. Annu. Rev. Entomol. 36, 65–89 (1991). Article  Google Scholar  2. Bowers, M. D. Iridoid glycosides and host-plant specificity in larvae of the buckeye butterfly, Junonia coenia (Nymphalidae). J. Chem. Ecol. 10, 1567–1577 (1984). CAS …

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WGCNA (TRAIT DATA)

WGCNA (TRAIT DATA) 0 I had already obtained a group of significant proteins after performing analysis on data obtained from LC-MS. I would like to perform network analysis on selected proteins using WGCNA package in R. Network analysis using WGCNA:- Removed outlier samples and Genes. Identified softpower (Beta) for singed…

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Getting data from TOM matrix (WGCNA)

Getting data from TOM matrix (WGCNA) 0 Hello, I would like to access the correlation in TOM matrix of a specific subset of genes. Manually, as it is a matrix, there’re no row/column names so I can’t identify the genes I’m looking for. In the manual, I’ve seen the function…

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The LpoA activator is required to stimulate the peptidoglycan polymerase activity of its cognate cell wall synthase PBP1a

Significance Class A penicillin-binding proteins (aPBPs) assemble the bacterial cell wall and are the targets of penicillin and related β-lactam antibiotics. In gram-negative bacteria, the aPBPs require outer membrane lipoproteins to function. However, little is known about how these proteins promote the activity of their cognate synthases in cells. Here,…

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pre-proccessing of RNAseq data for WGCNA

pre-proccessing of RNAseq data for WGCNA 0 Hi everyone, i wanted to create an expression matrix for WGCNA input. however, i has been said that use RPKM/FPKM data instead of CPM, how can i change my TCGA data to RPKM/FPKM in GDCquery and how to filter expression set of genes…

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WGCNA significant genes

Hi, I am using WGCNA to construct a network and find significant genes for a trait of interest. After making the network, I chose a module based on the pvalue and correlation value. Then I calculated gene significance values for all genes in that module. trait_x <- as.data.frame(datTraits[, “trait_x”, drop…

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Problems with downloading fastq files from sra-toolkit

Problems with downloading fastq files from sra-toolkit 1 I have been trying to download the fastq files of a single cell RNA experiment from SRX8632237 with the following SRA runs : SRR12108143 SRR12108144 SRR12108145 SRR12108146 The runs show that it has 3 reads per spot (link). However, I am unable…

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WGCNA for diferent stages (I-IV)

WGCNA for diferent stages (I-IV) 0 I wanted to share my issue with WGCNA. any help would be very valuable for me I wanted to know that for identifying modules related with Stage I to Stage IV, how can i binarize these stages into 0, 1, 2, 3, respectively? i…

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Predicting and characterizing a cancer dependency map of tumors with deep learning

INTRODUCTION The development of novel cancer therapies requires knowledge of specific biological pathways to target individual tumors and eradicate cancer cells. Toward this goal, the landscape of genetic vulnerabilities of cancer, or the cancer dependency map, is being systematically profiled. Using RNA interference (RNAi) loss-of-function screens, Marcotte et al. (1),…

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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…

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Strategies to learn about a gene of interest from single-cell RNA-seq data

Strategies to learn about a gene of interest from single-cell RNA-seq data 0 Using a large public single-cell RNA-seq dataset from brain where cells are already segregated by brain region, cell type, marker gene cluster, etc. I am looking to do exploratory analyses to learn whatever I can about a…

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Difference between linear and log2 CNA values

Difference between linear and log2 CNA values 0 Hi, Simply what the title is asking. Cbioportal allows for either Log2 cna values or linear cna values. Is this simply how the values were normalized? Is there a way to differentiate between the two value types by seeing the numbers? Thanks!…

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How filter genes to construct co-expression network?

How filter genes to construct co-expression network? 1 Hi, I am interested to filter data for constructing co-expression network , Which parameter can i use to filter genes? As i know in WGCNA tutorial, it suggests not to use differential expressed genes(DEG) to filter genes. WGCNA Co-expreesion network DEG Filtering…

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How to load Seurat Object into WGCNA Tutorial Format

As far as I can find, there is only one tutorial about loading Seurat objects into WGCNA (ucdavis-bioinformatics-training.github.io/2019-single-cell-RNA-sequencing-Workshop-UCD_UCSF/scrnaseq_analysis/scRNA_Workshop-PART6.html). I am really new to programming so it’s probably just my inexperience, but I am not sure how to load my Seurat object into a format that works with WGCNA’s tutorials (horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/)….

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Copy number differences between groups

Copy number differences between groups 0 Analogous to differential expression with RNA data, is there a statistic or tool to analyze the frequency of copy number alterations between two groups? I had imagined this to be a Chi-square performed like 20,000 times (each gene) to see if that particular gene…

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Agilent-016436 Human miRNA Microarray 1.0

Upon request, a quick tutorial for processing the Agilent micro-RNA (miRNA) microarray data of GSE28955. The raw TXT files are contained in: ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28955/suppl/GSE28955_RAW.tar Download this TAR file Unpack it [the TAR file] Unzip the txt.gz files Store these [txt files] in a directory raw/ Then, create a tab-delimited file, targets.txt,…

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Inventors of CRISPR Gene Editing Appointed to Pontifical Academy of Sciences| National Catholic Register

VATICAN CITY — Pope Francis has appointed the co-inventors of the CRISPR genome editing technology to the Pontifical Academy of Sciences.  Jennifer Doudna and Emmanuelle Charpentier, who discovered CRISPR fewer than ten years ago, were appointed to the Vatican’s scientific academy consecutively Aug. 10-11. Their discovery sparked research into new…

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