ArticleNucleic acids research2012
The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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
31 citing papers in PubMed, 1 synthesis or guideline pooled it.
- FH535, a β-catenin pathway inhibitor, represses pancreatic cancer xenograft growth and angiogenesis.Oncotarget · 2016Pooled it
- PSPC1-SMAD3 axis regulates iron-induced beiging of adipocytes in white adipose tissue.Cell communication and signaling : CCS · 2025Article
- Article
- Gene expression patterns associated with caudal fin shape in the cichlidHydrobiologia · 2023Article
- Large-scale analysis of Drosophila core promoter function using synthetic promoters.Molecular systems biology · 2022Article
- Article
- FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Regulatory motifs found in the small heat shock protein (sHSP) gene family in tomato.BMC genomics · 2018Article
- MODSIDE: a motif discovery pipeline and similarity detector.BMC genomics · 2018Article
- Towards a gene regulatory network shaping the fins of the Princess cichlid.Scientific reports · 2018Article
- Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.The ISME journal · 2018Article
- Performance evaluation for MOTIFSIM.Biological procedures online · 2018Article
- Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana.BMC genomics · 2017Article
- RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.Nucleic acids research · 2017Article
- NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.Nucleic acids research · 2017Article
- RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases.eLife · 2017Article
- Article
- Article
- The orientation of transcription factor binding site motifs in gene promoter regions: does it matter?BMC genomics · 2016Article
- ATtRACT-a database of RNA-binding proteins and associated motifs.Database : the journal of biological databases and curation · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The discovery of regulatory motifs enriched in sets of DNA or RNA sequences is fundamental to the analysis of a great variety of functional genomics experiments. These motifs usually represent binding sites of proteins or non-coding RNAs, which are best described by position weight matrices (PWMs). We have recently developed XXmotif, a de novo motif discovery method that is able to directly optimize the statistical significance of PWMs. XXmotif can also score conservation and positional clustering of motifs. The XXmotif server provides (i) a list of significantly overrepresented motif PWMs with web logos and E-values; (ii) a graph with color-coded boxes indicating the positions of selected motifs in the input sequences; (iii) a histogram of the overall positional distribution for selected motifs and (iv) a page for each motif with all significant motif occurrences, their P-values for enrichment, conservation and localization, their sequence contexts and coordinates. Free access: http://xxmotif.genzentrum.lmu.de.
Indexed as
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.