ArticlePLoS computational biology2012
Exploring massive, genome scale datasets with the GenometriCorr package.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
What it found
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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.
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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.
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Who cites it
125 citing papers in PubMed.
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- BiGvCL: bipartite graph-based cross-domain contrastive learning model for the predicting drug-gene interactions.Briefings in bioinformatics · 2026Article
- Episodic and Ongoing Mechanisms Drive Plastid-Derived Nuclear DNA Evolution in Angiosperms.Genome biology and evolution · 2025Article
- Article
- NKX2-5 congenital heart disease mutations show diverse loss and gain of epigenomic, biochemical and chromatin search functions underpinning pathogenicity.bioRxiv : the preprint server for biology · 2025Article
- Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones.Genome biology · 2025Article
- PBRM1 directs PBAF to pericentromeres and protects centromere integrity.Nature communications · 2025Article
- Multilevel Gene Expression Changes in Lineages Containing Adaptive Copy Number Variants.Molecular biology and evolution · 2025Article
- Transcriptional co-regulator OCA-B/Pou2af1 restricts Th2 differentiation.Frontiers in immunology · 2025Article
- Interaction of methyl-CpG-binding protein 2 (MeCP2) with distinct enhancers in the mouse cortex.Nature neuroscience · 2025Article
- Exploration and Enrichment Analysis of the QTLome for Important Traits in Livestock Species.Genes · 2024Article
- Targeting the chromatin binding of exportin-1 disrupts NFAT and T cell activation.Nature chemical biology · 2024Article
- Regulatory transposable elements in the encyclopedia of DNA elements.Nature communications · 2024Article
- Multilevel gene expression changes in lineages containing adaptive copy number variants.bioRxiv : the preprint server for biology · 2024Article
- Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency.Nature communications · 2024Article
- BaRDIC: robust peak calling for RNA-DNA interaction data.NAR genomics and bioinformatics · 2024Article
- Tho2 is critical for the recruitment of Rrp6 to chromatin in response to perturbed mRNP biogenesis.RNA (New York, N.Y.) · 2023Article
- HiCognition: a visual exploration and hypothesis testing tool for 3D genomics.Genome biology · 2023Article
- NuRD-independent Mi-2 activity represses ectopic gene expression during neuronal maturation.EMBO reports · 2023Article
- Connectome and regulatory hubs of CAGE highly active enhancers.Scientific reports · 2023Article
65 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
unlabelledWe have created a statistically grounded tool for determining the correlation of genomewide data with other datasets or known biological features, intended to guide biological exploration of high-dimensional datasets, rather than providing immediate answers. The software enables several biologically motivated approaches to these data and here we describe the rationale and implementation for each approach. Our models and statistics are implemented in an R package that efficiently calculates the spatial correlation between two sets of genomic intervals (data and/or annotated features), for use as a metric of functional interaction. The software handles any type of pointwise or interval data and instead of running analyses with predefined metrics, it computes the significance and direction of several types of spatial association; this is intended to suggest potentially relevant relationships between the datasets. AVAILABILITY AND IMPLEMENTATION: The package, GenometriCorr, can be freely downloaded at http://genometricorr.sourceforge.net/. Installation guidelines and examples are available from the sourceforge repository. The package is pending submission to Bioconductor.
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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.