Tag: fimo
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer
Mice The research conducted in this study complied with all of the relevant ethical regulations. The animal protocols were approved by and performed in accordance with the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. C57BL/6, OT-I50, pmel51 and Rosa26-Cas9 knock-in52 mice were purchased from The…
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)….
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…
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…
Introduction to Bioinformatics in Transcriptomics and Gene Expression Analysis
Bioinformatics is a field that has revolutionized the way we analyze biological data. It has played a crucial role in the analysis of transcriptomics and gene expression data. Transcriptomics is the study of the transcriptome, which is the complete set of RNA transcripts produced by the genome of an organism….
Finding TF motifs enriched in series of ATAC-seq peaks (using fimo?)
Finding TF motifs enriched in series of ATAC-seq peaks (using fimo?) 1 Hi all, I have a series of peaks located in a .txt file (chr / start / end) and would like to know if there are tf motifs enriched in each of the individual peaks. For eg, I…
Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei
Bacterial strains and cultivation Twenty-eight L. paracasei isolates (including L. paracasei Zhang) and a pglX gene-inactivated strain of L. paracasei Zhang were obtained from the Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, at the Inner Mongolia Agricultural University of China. For strain activation, the bacteria were cultivated…
The little skate genome and the evolutionary emergence of wing-like fins
Nakamura, T. et al. Molecular mechanisms underlying the exceptional adaptations of batoid fins. Proc. Natl Acad. Sci. USA 112, 15940–15945 (2015). Article ADS CAS PubMed PubMed Central Google Scholar Turner, N. et al. The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids. Proc. Biol. Sci….
Antismash on Fasta files
Hello, you can provide FASTA files to it ########### antiSMASH 6.1.1 ############# usage: antismash [–taxon {bacteria,fungi}] [–output-dir OUTPUT_DIR] [–output-basename OUTPUT_BASENAME] [–reuse-results PATH] [–limit LIMIT] [–minlength MINLENGTH] [–start START] [–end END] [–databases PATH] [–write-config-file PATH] [–without-fimo] [–executable-paths EXECUTABLE=PATH,EXECUTABLE2=PATH2,…] [–allow-long-headers] [-v] [-d] [–logfile PATH] [–list-plugins] [–check-prereqs] [–limit-to-record RECORD_ID] [-V] [–profiling] [–skip-sanitisation] [–skip-zip-file]…
Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection
Bergwerk, M. et al. Covid-19 breakthrough infections in vaccinated health care workers. N. Engl. J. Med. 385, 1474–1484 (2021). Article CAS PubMed Google Scholar V’Kovski, P., Kratzel, A., Steiner, S., Stalder, H. & Thiel, V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat. Rev. Microbiol. 19, 155–170 (2021). Article PubMed …
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…
Transcription Factor Functions
Transcription Factor Functions 1 I have been wondering if there is a database that contains information about whether a transcription factor has a repressive or an activating or a context-dependent function. factor database transcription • 71 views If you performed a whole-genome FIMO scan, selecting those hits that match your…
MEME suite compare motifs between species
MEME suite compare motifs between species 1 Hello, I have a set of 5kb sequences upstream of a gene from different primates, and I would like to know what motifs are in enhancers and promoters of primates vs the 5kb upstream sequences of a set of the same gene but…
Exporting list of enriched motif sequences from CentriMo in MEME Suite
Hi, I have a set of sequences for which I have identified a list of significant motifs through MEME. I then used FIMO to find specific regions in my sequences where the identified significant motifs were enriched. It gives me enriched locations for my motifs. It does not give me…
How to graphically represent a known DNA motif in a list of DNA sequences
How to graphically represent a known DNA motif in a list of DNA sequences 0 Hello. I was using FIMO to search a known motif in a list of genes. FIMO gives me a list of motif occurences, that is the matched sequence, the p-value, the q-value and also the…