Tag: JASPAR

Researcher/Postdoc to enhance computational resources for regulatory genomics with deep learning

Description: The Computational Biology & Gene Regulation group led by Anthony Mathelier at the NCMM, a part of the Nordic EMBL Partnership for Molecular Medicine, is seeking a highly motivated Researcher or Postdoctoral Fellow for a two-year position, starting as soon as possible in 2024. The selected candidate will play…

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Highly dynamic inflammatory and excitability transcriptional profiles in hippocampal CA1 following status epilepticus

Dynamic mRNA signatures in the early phase of epileptogenesis after Pilocarpine-induced SE To decipher transcriptional changes early after pilocarpine-induced SE in the hippocampal CA1 subfield, we compared mRNA expression profiles of pilocarpine-induced SE animals and non-SE controls in hippocampal CA1 at five different time points, i.e. 6, 12, 24, 36…

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A vertebrate-wide catalogue of T1R receptors reveals diversity in taste perception

Identification of novel TAS1R family members We identified homologues of TAS1R genes that are included in public genome/transcriptome databases for diverse taxa of jawed vertebrates (Supplementary Table 1). Except for jawed vertebrates, TAS1R genes were not identified in any Deuterostomia reference genomes (lampreys, hagfishes, tunicates, lancelets, sea urchins, starfish, hemichordate,…

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Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

     Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…

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DNA methylation change in blood cells of FB and CFS patients

Introduction Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) are characterized by chronic pain, fatigue, and weakness. Patients with these symptoms also suffer from sleep abnormalities and report affected cognitive processes such as memory. The diagnosis of these two syndromes is challenging and is based on questionnaires that make the diagnosis…

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Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article  PubMed  Google Scholar  Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article  PubMed  Google Scholar  Amborella Genome Project et al. The Amborella…

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GDF11 slows excitatory neuronal senescence and brain ageing by repressing p21

Experimental model and subject details Mice Male ICR mice (Laboratory Animal Center of Zhejiang Academy of Medical Sciences) at age of 3 months (M), 9 M and 36 M, male C57BL/B6 wild‐type (WT) mice (Shanghai Slac Laboratory) at age of 3 M and 10 M, male GDF11-flox mice (GDF11f/f, mice carrying the “floxed” GDF11…

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MICA: a multi-omics method to predict gene regulatory networks in early human embryos

Introduction After the fusion of the oocyte and sperm, the zygote undergoes a series of cell divisions until it forms a blastocyst before implantation into the uterus. A human blastocyst is formed of a fluid-filled cavity and ∼200 cells that comprise three distinct cell types: the trophectoderm (TE), which gives…

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Mouse mm10 chr4:22,481,383-22,489,763 UCSC Genome Browser v455

     Custom Tracks Adiposehidedensesquishpackfull Cerebellumhidedensesquishpackfull Cortexhidedensesquishpackfull Liverhidedensesquishpackfull Lunghidedensesquishpackfull Sintesthidedensesquishpackfull Spleenhidedensesquishpackfull    mouse_7_core ATAC Adipose Rep1hidedensefull ATAC Adipose Rep2hidedensefull ATAC Cerebellum Rep1hidedensefull ATAC Cerebellum Rep2hidedensefull ATAC Colon Rep1hidedensefull ATAC Colon Rep2hidedensefull ATAC Cortex Rep1hidedensefull ATAC Cortex Rep2hidedensefull ATAC Heart Rep1hidedensefull ATAC Heart Rep2hidedensefull ATAC Liver Rep1hidedensefull ATAC Liver Rep2hidedensefull ATAC…

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Bioconductor – JASPAR2020 (development version)

DOI: 10.18129/B9.bioc.JASPAR2020   This is the development version of JASPAR2020; for the stable release version, see JASPAR2020. Data package for JASPAR database (version 2020) Bioconductor version: Development (3.18) Data package for JASPAR2020. To search this databases, please use the package TFBSTools (>= 1.23.1). Author: Damir Baranasic <damir.baranasic at lms.mrc.ac.uk> Maintainer:…

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Transcriptional regulation and overexpression of GST cluster enhances pesticide resistance in the cotton bollworm, Helicoverpa armigera (Lepidoptera: Noctuidae)

Bras, A., Roy, A., Heckel, D. G., Anderson, P. & Green, K. K. Pesticide resistance in arthropods: ecology matters too. Ecol. Lett. 25, 1746–1759 (2022). Article  PubMed  PubMed Central  Google Scholar  Chen, Y. H. & Schoville, S. D. Editorial overview: ecology: ecological adaptation in agroecosystems: novel opportunities to integrate evolutionary…

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Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains | Cell & Bioscience

Lo MT, Kauppi K, Fan CC, Sanyal N, Reas ET, Sundar VS, Lee WC, Desikan RS, McEvoy LK, Chen CH, Alzheimer’s Disease Genetics, C. Identification of genetic heterogeneity of Alzheimer’s disease across age. Neurobiol Aging. 2019;84(243):e241-243. doi.org/10.1016/j.neurobiolaging.2019.02.022. Article  Google Scholar  Nacmias B, Bagnoli S, Piaceri I, Sorbi S. Genetic heterogeneity…

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plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style | BMC Genomics

Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990;18(20):6097–100. Article  CAS  PubMed  PubMed Central  Google Scholar  Colaert N, Helsens K, Martens L, Vandekerckhove J, Gevaert K. Improved visualization of protein consensus sequences by iceLogo. Nat Methods. 2009;6(11):786–7. Article  CAS  PubMed  Google Scholar …

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Methamphetamine-induced region-specific transcriptomic and epigenetic changes in the brain of male rats

Jayanthi, S., McCoy, M. T. & Cadet, J. L. Epigenetic Regulatory Dynamics in Models of Methamphetamine-Use Disorder. Genes 12, 1614 (2021). Article  CAS  Google Scholar  Meredith, C. W., Jaffe, C., Ang-Lee, K. & Saxon, A. J. Implications of chronic methamphetamine use: a literature review. Harv. Rev. Psychiatry 13, 141–154 (2005)….

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Thymic mimetic cells function beyond self-tolerance

Klein, L., Kyewski, B., Allen, P. M. & Hogquist, K. A. Positive and negative selection of the T cell repertoire: what thymocytes see (and don’t see). Nat. Rev. Immunol. 14, 377–391 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  Bornstein, C. et al. Single-cell mapping of the thymic stroma identifies…

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Scanning a genomic region for TFBS

I have an answer posted on the Bioinformatics SE that suggests how to use FIMO to scan for TFBS over a genome: bioinformatics.stackexchange.com/a/2491/776 This example uses UCSC to retrieve sequence information, JASPAR for MEME-formatted motif models, and BEDOPS starch to compress the results (which will be sizeable). Once you have…

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Molecular features driving cellular complexity of human brain evolution

King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107–116 (1975). Article  ADS  CAS  PubMed  Google Scholar  Konopka, G. et al. Human-specific transcriptional networks in the brain. Neuron 75, 601–617 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Liu, X. et al….

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Identify binding motifs within large super enhancer region

Identify binding motifs within large super enhancer region 1 Hello, From my H3K27ac ChIP seq data, I have identified 500 super enhancer regions using Homer’s findPeaks -style super. From the super enhancer regions, I found 4 enriched binding motifs within the 500 super enhancer regions using Homer’s findMotifsGenome.pl. First, I…

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Identification of macrophage-related genes in sepsis-induced ARDS using bioinformatics and machine learning

Screening of differentially expressed genes in GSE32707 According to the screening criteria of differentially expressed genes, there were 489 differentially expressed genes between the control and sepsis groups, of which 152 genes were downregulated in sepsis patients and 337 genes were upregulated in sepsis patients (Fig. 1A). In contrast, there were…

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Bioinformatics and system biology approach to identify potential common pathogenesis for COVID-19 infection and osteoarthritis

Hunter, D. J. & Bierma-Zeinstra, S. Osteoarthritis. Lancet 393, 1745–1759 (2019). Article  CAS  PubMed  Google Scholar  Puig-Junoy, J. & Ruiz Zamora, A. Socio-economic costs of osteoarthritis: A systematic review of cost-of-illness studies. Semin. Arthritis Rheum. 44, 531–541 (2015). Article  PubMed  Google Scholar  Hunter, D. J., March, L. & Chew, M….

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The digital dark matter clouding AI in genome analysis

Visualizing the gradient correction. Sequence logo of the uncorrected saliency map (top row), gradient angles at each position (second row), and corrected saliency map (third row) for a patch from representative test sequences. a, b CNN-deep-relu trained to make binary predictions on a synthetic data and b ChIP-seq data for ATF2 protein in GM12878….

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Annotating and prioritizing human non-coding variants with RegulomeDB v.2

Nearly 90% of the disease risk-associated variants identified by genome-wide association studies are in non-coding regions of the genome. The annotations obtained by analyzing functional genomics assays can provide additional information to pinpoint causal variants, which are often not the lead variants identified from association studies. However, the lack of…

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Human hg38 chr10:21,513,475-21,525,682 UCSC Genome Browser v446

     Seq2science ChIP-seq hub ChIP-seqhidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 updated Fix Patcheshidedensesquishpackfull p14 updated Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19 Diffhidedensesquishpackfull INSDChidedensesquishpackfull LiftOver & ReMaphidedensesquishpackfull LRG Regionshidedensesquishpackfull Mappabilityhideshow Problematic Regionshidedensesquishpackfull new Recomb…

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Ras interacting protein 1 facilitated proliferation and invasion of diffuse large B-cell lymphoma cells

Introduction Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma, accounting for 30% of non-Hodgkin’s lymphoma. Approximately 150,000 new cases are diagnosed annually worldwideCitation1. DLBCL is characterized by heterogeneity, aggressiveness, and frequent relapse or resistance to chemotherapyCitation2. Due to the heterogeneity of DLBCL, the immunological, pathological, molecular, and genetic…

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Mapping of JASPAR motif to genes

Mapping of JASPAR motif to genes 0 Hello everyone I am using Jaspar motifs for my analysis. I need to create a input file which links motifs with their annotated gene ids. example : Alx1 ENSG00000180318 ALX3 ENSG00000156150 Alx4 ENSG00000052850 Ar ENSG00000169083 AR ENSG00000169083 ARGFX ENSG00000186103 Arid3a ENSG00000116017 Is there…

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CTCF: an R/bioconductor data package of human and mouse CTCF binding sites

. 2022 Dec 16;2(1):vbac097. doi: 10.1093/bioadv/vbac097. eCollection 2022. Affiliations Expand Affiliations 1 Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA. 2 Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA. 3 Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA. 4 Curriculum in…

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Best Database Of Transcription Factor Binding Sites

Best Database Of Transcription Factor Binding Sites 8 (a) Which is the best database for transcription factor binding site, TRANSFAC or JASPAR? Why? (b) Is it still valid to assume, “transcription factor binding sites are only present in 5’UTR and in promoter region”? Note: kindly put references in your answer….

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Annelid functional genomics reveal the origins of bilaterian life cycles

Hall, B. K. & Wake, M. H. in The Origin and Evolution of Larval Forms (eds Hall, B. K. & Wake, M. H.) 1–19 (Academic Press, 1999). Nielsen, C. Animal phylogeny in the light of the trochaea theory. Biol. J. Linn. Soc. 25, 243–299 (2008). Article  Google Scholar  Garstang, W….

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Human hg38 chr19:11,216,461-11,670,150 UCSC Genome Browser v442

     Custom Tracks 1806hidedensefull 468hidedensefull BT20hidedensefull BT474hidedensefull MCF7hidedensefull T47Dhidedensefull    Mapping and Sequencing Base Positionhidedensefull p13 Fix Patcheshidedensesquishpackfull p13 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19 Diffhidedensesquishpackfull INSDChidedensesquishpackfull LiftOver & ReMaphidedensesquishpackfull LRG Regionshidedensesquishpackfull Mappabilityhideshow RefSeq Acchidedensesquishpackfull…

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Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

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FBXO9 Mediates the Cancer-Promoting Effects of ZNF143 by Degrading FBXW7 and Facilitates Drug Resistance in Hepatocellular Carcinoma

doi: 10.3389/fonc.2022.930220. eCollection 2022. Zhenyu Wang  1 , Xiaoxia Chen  1   2 , Lianer Zhou  1 , Xinge Zhao  1 , Chao Ge  1 , Fangyu Zhao  1 , Haiyang Xie  3 , Taoyang Chen  4 , Hua Tian  1 , Hong Li  1 , Jinjun Li  1 Affiliations Expand Affiliations 1 State Key Laboratory of Oncogenes and Related…

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Workflow Platforms for Systems Genetics

Workflow Platforms for Systems Genetics eQTL Platforms eQTL Viewer Mouse Genome Informatics: Phenotypes, Alleles & Disease Models PhenoGen Informatics (CO U) eXtensible Genotype And Phenotype platform (XGAP) MOLGENIS & MetaNetwork, Swertz & Jansen, U Groningen Weighted Gene Co-expression Network Analysis (WGCNA), Horvath, UCLA iPlant Sage Bionetworks Repository: Synapse GenomeSpace Institute…

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SNP2TFBS

SNP2TFBS Viewing variants that affect TF binding – Results – SNP identifier Chrom id (Feb 2009 GRCh37/hg19) SNP position NB. of TF factors rs1800629   dbSNP NC_000006.11 (chr6) 31543031 1 TF name  PWM score on Ref PWM score on Alt Score difference Low Score Thr High Score Thr MZF1_1-4  1024  ….

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Bioconductor – MotIV

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MotIV. Motif Identification and Validation Bioconductor version: 3.4 This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize…

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Problem with HOMER -find

Problem with HOMER -find <motif file> 0 I am trying to search for specific motifs in my set of promoters. It should be possible with the option -find *.motif I know that there are for sure some occurrences because I have found them with search function in Notepad. However HOMER…

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