Tag: KO

r – Can I analyze RNAseq data from two different cell types using the design matrix model.matrix(~0 + group + celltype)?

I have two cell types(11C and 13C) and two groups (KO and CTRL). sample celltype group 11C-17 11C KO 11C-84 11C KO 11C-C 11C CTRL 13C-17 13C KO 13C-84 13C KO 13C-C 13C CTRL As shown in the PCA plot, the cell type is the dominant difference. But, I’d like…

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KEGG T00007: b1542

Entry b4323             CDS       T00007                                  Symbol uxuB Name (RefSeq) D-mannonate oxidoreductase   KO K00040   fructuronate reductase [EC:1.1.1.57] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00040   Pentose and glucuronate interconversions eco01100   Metabolic pathways Module eco_M00061   D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P Brite KEGG Orthology (KO) [BR:eco00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    b4323 (uxuB)Enzymes…

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A cell-based phenotypic library selection and screening approach for the de novo discovery of novel functional chimeric antigen receptors

Cell lines and culture Unless stated otherwise, all tumor target cell lines were sourced from the ATCC via LGC Standards. Human endogenous mesothelin (MSLN)-positive target cell lines H-226 (lung carcinoma, MSLN+, ATCC® CRL-5826™) and AsPC-1 (ATCC CRL-1682), and MSLN-negative Raji control cells (ATCC CCL-86) were cultured in RPMI-1640 Glutamax (Life Technologies,…

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Entheon Biomedical Subsidiary, HaluGen Life Sciences, Announces Agreement with Psychedelics Today

Expanding brand awareness and access to HaluGen’s Psychedelics Genetic Test Kit Vancouver, British Columbia–(Newsfile Corp. – January 18, 2022) – Entheon Biomedical Corp. (CSE: ENBI) (OTCQB: ENTBF) (FSE: 1XU1) (“Entheon” or the “Company“), a biomedical company focused on the research and development of psychedelic drugs and leading-edge biomarkers to provide…

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Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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The Genetic Architecture of Sleep Health Scores in the UK

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

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KEGG ORTHOLOGY: K11868

KEGG ORTHOLOGY: K11868     ORTHOLOGY: K11868 Help Entry K11868                      KO                                      Symbol CYP71A13 Name indoleacetaldoxime dehydratase [EC:4.8.1.3] Pathway Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism  09105 Amino acid metabolism   00380 Tryptophan metabolism    K11868  CYP71A13; indoleacetaldoxime dehydratase 09180 Brite Hierarchies  09181 Protein families: metabolism   00199 Cytochrome P450    K11868  CYP71A13; indoleacetaldoxime dehydrataseEnzymes [BR:ko01000] 4. Lyases  4.8  Nitrogen-oxygen lyases   4.8.1  Hydro-lyases    4.8.1.3  indoleacetaldoxime dehydratase     K11868  CYP71A13; indoleacetaldoxime dehydrataseCytochrome P450 [BR:ko00199] Cytochrome P450, plant type  CYP71 family   K11868  CYP71A13;…

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KEGG T01005: 453503

Entry 453503            CDS       T01005                                  Symbol SNX1 Name (RefSeq) sorting nexin-1 isoform X3   KO K17917   sorting nexin-1/2 Organism ptr  Pan troglodytes (chimpanzee) Pathway ptr04144   Endocytosis Brite KEGG Orthology (KO) [BR:ptr00001] 09140 Cellular Processes  09141 Transport and catabolism   04144 Endocytosis    453503 (SNX1) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:ptr04131]    453503 (SNX1)  09183 Protein families: signaling and cellular processes   04990…

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Phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein PINLYP regulates type I interferon innate immunity

Significance Interferon (IFN)-mediated antiviral responses serve as the first line of the host innate immune defense against viral infection. Here we identify a previously uncharacterized protein designated phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein (PINLYP), which is essential for embryonic development and plays an important role in type I IFN…

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KEGG ORTHOLOGY: K02207

Brite KEGG Orthology (KO) [BR:ko00001] 09120 Genetic Information Processing  09123 Folding, sorting and degradation   04120 Ubiquitin mediated proteolysis    K02207  UBE2R, UBC3, CDC34; ubiquitin-conjugating enzyme E2 R 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04121 Ubiquitin system    K02207  UBE2R, UBC3, CDC34; ubiquitin-conjugating enzyme E2 REnzymes [BR:ko01000] 2. Transferases  2.3  Acyltransferases   2.3.2  Aminoacyltransferases    2.3.2.23  E2 ubiquitin-conjugating enzyme     K02207  UBE2R, UBC3, CDC34; ubiquitin-conjugating enzyme E2 RUbiquitin system [BR:ko04121] Ubiquitin-conjugating enzymes (E2)  Ubiquitin-conjugating…

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Zooplankton diversity monitoring strategy for the urban coastal region using metabarcoding analysis

1. Eyun, S. Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies. BMC Evol. Biol. 17, 23 (2017). PubMed  PubMed Central  Google Scholar  2. Eyun, S. et al. Evolutionary history of chemosensory-related gene families across the Arthropoda. Mol. Biol. Evol. 34, 1838–1862 (2017). CAS  PubMed …

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Establishment of sunitinib-resistant CDX model of ccRCC

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease

Significance Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic…

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A protein bridging the gap between sea urchin generations

In the second half of the 1800s biologists began to investigate the cellular basis of development. Sea urchins became a favorite material for this endeavor because their gametes can be obtained in vast numbers and fertilization and development are external to the adult body. The first research on fertilization centered…

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GREAT genome ontology top hits criteria?

GREAT genome ontology top hits criteria? 0 Hi, when running a GREAT analysis of a bed file using the default settings, what are the criteria by which the top few hits are shown in each of the gene ontology categories? For example, in ‘mouse phenotype single KO’ I get 8…

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GREAT difference between ‘mouse phenotype’ and ‘mouse phenotype single KO’

GREAT difference between ‘mouse phenotype’ and ‘mouse phenotype single KO’ 0 Hi, I’ve been trying to find information on what the difference is between the ‘mouse phenotype’ and ‘mouse phenotype single KO’ categories that are generated in GREAT genome ontology analyses but haven’t been able to find any detailed explanation….

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kegg pathway database

Pathways that include all genes in gene_ids. Here the KEGG API operations are explained in comparison to these web tools. MODULE — modules or functional units of genes, BRITE — hierarchical classifications of biological entities, This page was last edited on 22 October 2020, at 18:43. The list can be…

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Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Significance The collection of large amounts of whole-genome sequencing data allowed for identification of mutational signatures, which are characteristic combinations of substitutions in the context of neighboring bases. The clinical significance of these mutational signatures is still largely unknown. In neuroblastoma, we showed that high levels of cytosine > adenine…

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copper c19520 in rok

CHAPTER 4 COPPER AND COPPER ALLOYS – PDF Free Download 80 196 Copper and Copper Alloys Table 43 Velocity Guidelines for Copper Alloys in Pumps and Propellers Operating in Seawater UNS Alloy Number Peripheral Velocity ft/s m/s C C C90300 C C95200 C C95500 C95700 C Source: Copper Development Association….

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Antibiotic Resistance Genes | IDR

Witawat Tunyong,1 Weewan Arsheewa,2 Sirijan Santajit,3,4 Thida Kong-ngoen,1 Pornpan Pumirat,1 Nitat Sookrung,5,6 Wanpen Chaicumpa,6 Nitaya Indrawattana1 1Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand; 2Department of Microbiology, Phrapokklao Hospital, Chanthaburi, 22000, Thailand; 3School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, 80161, Thailand;…

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Genome-wide synthetic lethal screen unveils novel CAIX-NFS1/xCT axis as a targetable vulnerability in hypoxic solid tumors

Abstract The metabolic mechanisms involved in the survival of tumor cells within the hypoxic niche remain unclear. We carried out a synthetic lethal CRISPR screen to identify survival mechanisms governed by the tumor hypoxia–induced pH regulator carbonic anhydrase IX (CAIX). We identified a redox homeostasis network containing the iron-sulfur cluster…

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Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance

1. Lee, M.-R. et al. Mycobacterium abscessus complex infections in humans. Emerg. Infect. Dis. 21, 1638–1646 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Prince, D. S. et al. Infection with Mycobacterium avium complex in patients without predisposing conditions. N. Engl. J. Med. 321, 863–868 (1989). CAS  PubMed  Article  Google…

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How to compute module completion ratio of KEGG modules from KO identifiers? (command line)

How to compute module completion ratio of KEGG modules from KO identifiers? (command line) 0 I was previously using KEGG-MAPLE to compute module completion ratios for metagenome assembled genomes. However, this tool was web only (very frustrating) and also it has been discontinued. Now I’m trying to do something similar…

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Plasmid-Encoded VIM-2-pProducing Pseudomonas stutzeri | IDR

Introduction Pseudomonas stutzeri is an aerobic, nonfermenting, active, Gram-negative oxidase-positive bacterium with unique colony morphology.1,2 Burri and Stutzer first described it in 1985,3 and the specific metabolic properties, such as denitrification, degradation of aromatic compounds, and nitrogen fixation, distinguish it from other pseudomonads species.2,4 Historically, P. stutzeri was not commonly…

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Error creating DESeq2 Data Set from HTSeq-Count

I am trying to run DESeq2 using gene counts generated by HTSeq-Count. I combine files for different conditions: directory <- “~/GeneCountFiles/” WT_Files <- c( “P0CTRS3.aligned.sam.genecount”, “P0CTRS4.aligned.sam.genecount”, “P0CTRS5.aligned.sam.genecount” ) KO_Files <- c( “P0CTRS1.aligned.sam.genecount”, “P0CTRS2.aligned.sam.genecount”, “P0CTRS6.aligned.sam.genecount” ) I then create the sample table: sampleTable <- data.frame( sampleName=c(WT_Files, KO_Files), fileName=c(WT_Files, KO_Files), genotype=c(rep(“WT”, length(WT_Files)),…

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graph datasets kaggle

This graph is pretty big, for global graph queries you’d need a page-cache of 6G and heap of 16G to work with it. bar_chart Datasets. Found insideWith this practical book, you’ll learn how to design and implement a graph database that brings the power of graphs to bear on a…

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Non-symmetric MA-plot (DESeq2)

Non-symmetric MA-plot (DESeq2) 0 Hello, I performed differential analysis of RNA-Seq using DESeq2 of mouse samples, with different genotype (WT and KO) and diet (CD and HFD). I expecting to have a lot of differential expressed genes (because of strong macroscopy differences), but I found MA plot are non-symmetric (“Raw…

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How to limit KAAS pathway results to certain species?

How to limit KAAS pathway results to certain species? 0 I’m working on a dataset in an insect species. I was using KAAS to annotate the genes. In the parameter for “GENES data set”, I only selected some species from insects. But in the results, the Pathway Mapping gave pathways…

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Assessing how similar/ different of activated pathways between multiple groups of samples

Assessing how similar/ different of activated pathways between multiple groups of samples 0 May I know are there is any bioinformatics package (or method) that can do a statistical test on two or multiple groups of pathway analysis. I have 4 conditions: Wild-type, control Wild-type, treatment knockout, control knockout, treatment…

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My bioinformatics story

My bioinformatics story 1 Hi all! I am new to the bioinformatics world and due to circumstances I have been given the complete responsibility to perform a human transciptomics data-analysis without bioinformatic background and for now also without supervision. This whole project feels like a big challenge, finding a puzzle…

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How to retrieve KO IDs for a list of genes?

How to retrieve KO IDs for a list of genes? 2 Hi, community!!! I have downloaded a list of genes from the MetaCyc database for some bacterial species. I want to find out their respective KO IDs. Can anyone please tell me how can I do that? Thanks KEGG database…

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