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…

Continue Reading Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer

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)….

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

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…

Continue Reading Scanning a genomic region for TFBS

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…

Continue Reading Identify binding motifs within large super enhancer region

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….

Continue Reading Introduction to Bioinformatics in Transcriptomics and Gene Expression Analysis

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…

Continue Reading Finding TF motifs enriched in series of ATAC-seq peaks (using fimo?)

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…

Continue Reading Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei

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….

Continue Reading The little skate genome and the evolutionary emergence of wing-like fins

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]…

Continue Reading Antismash on Fasta files

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 …

Continue Reading Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection

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…

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

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…

Continue Reading Transcription Factor Functions

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…

Continue Reading MEME suite compare motifs between species

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…

Continue Reading Exporting list of enriched motif sequences from CentriMo in MEME Suite

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…

Continue Reading How to graphically represent a known DNA motif in a list of DNA sequences