ArticleNAR genomics and bioinformatics2023
Quantifying the arms race between LINE-1 and KRAB-zinc finger genes through TECookbook.
Article in NAR genomics and bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
5 citing papers in PubMed, 4 citations in OpenAlex.
- Development and validation of a novel glioblastoma prognostic model: identifying STOX1 and ZNF248 as ferroptosis-related biomarkers.Cancer cell international · 2025Article
- Transposable element 5mC methylation state of blood cells predicts age and disease.Nature aging · 2025Article
- piRNA Defense Against Endogenous Retroviruses.Viruses · 2024Review
- Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective.Annual review of genomics and human genetics · 2024Review
- Integration of bioinformatics analysis reveals ZNF248 as a potential prognostic and immunotherapeutic biomarker for LIHC: machine learning and experimental evidence.American journal of cancer research · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To defend against the invasion of transposons, hundreds of KRAB-zinc finger genes (ZNFs) evolved to recognize and silence various repeat families specifically. However, most repeat elements reside in the human genome with high copy numbers, making the ChIP-seq reads of ZNFs targeting these repeats predominantly multi-mapping reads. This complicates downstream data analysis and signal quantification. To better visualize and quantify the arms race between transposons and ZNFs, the R package TECookbook has been developed to lift ChIP-seq data into reference repeat coordinates with proper normalization and extract all putative ZNF binding sites from defined loci of reference repeats for downstream analysis. In conjunction with specificity profiles derived from
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.