ArticleBMC proceedings2009
sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters.
Article in BMC proceedings, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources.BMC genomics · 2011Pooled it
- Identification of the Efficacy of Ex Situ Conservation ofPlants (Basel, Switzerland) · 2023Article
- Article
- Article
- The fetal ovary exhibits temporal sensitivity to a 'real-life' mixture of environmental chemicals.Scientific reports · 2016Article
- Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics.Frontiers in immunology · 2015Article
- The Longissimus and Semimembranosus muscles display marked differences in their gene expression profiles in pig.PloS one · 2014Article
- Dendritic cell subtypes from lymph nodes and blood show contrasted gene expression programs upon Bluetongue virus infection.Journal of virology · 2013Article
- Transcriptomic profiling of proteases and antiproteases in the liver of sexually mature hens in relation to vitellogenesis.BMC genomics · 2012Article
- Canine recombinant adenovirus vector induces an immunogenicity-related gene expression profile in skin-migrated CD11b⁺ -type DCs.PloS one · 2012Article
- Transcriptional responses of resistant and susceptible fish clones to the bacterial pathogen Flavobacterium psychrophilum.PloS one · 2012Article
- Infection of nonhost species dendritic cells in vitro with an attenuated myxoma virus induces gene expression that predicts its efficacy as a vaccine vector.Journal of virology · 2011Article
- Transcriptomic analysis of milk somatic cells in mastitis resistant and susceptible sheep upon challenge with Staphylococcus epidermidis and Staphylococcus aureus.BMC genomics · 2011Article
- Gene expression patterns in four brain areas associate with quantitative measure of estrous behavior in dairy cows.BMC genomics · 2011Article
- SigReannot-mart: a query environment for expression microarray probe re-annotations.Database : the journal of biological databases and curation · 2011Article
- Regional regulation of transcription in the bovine genome.PloS one · 2011Article
- A factor model to analyze heterogeneity in gene expression.BMC bioinformatics · 2010Article
- Using transcriptome profiling to characterize QTL regions on chicken chromosome 5.BMC genomics · 2009Article
- The EADGENE and SABRE post-analyses workshop.BMC proceedings · 2009Article
- Methods for interpreting lists of affected genes obtained in a DNA microarray experiment.BMC proceedings · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroarray is a powerful technology enabling to monitor tens of thousands of genes in a single experiment. Most microarrays are now using oligo-sets. The design of the oligo-nucleotides is time consuming and error prone. Genome wide microarray oligo-sets are designed using as large a set of transcripts as possible in order to monitor as many genes as possible. Depending on the genome sequencing state and on the assembly state the knowledge of the existing transcripts can be very different. This knowledge evolves with the different genome builds and gene builds. Once the design is done the microarrays are often used for several years. The biologists working in EADGENE expressed the need of up-to-dated annotation files for the oligo-sets they share including information about the orthologous genes of model species, the Gene Ontology, the corresponding pathways and the chromosomal location.
resultsThe results of SigReannot on a chicken micro-array used in the EADGENE project compared to the initial annotations show that 23% of the oligo-nucleotide gene annotations were not confirmed, 2% were modified and 1% were added. The interest of this up-to-date annotation procedure is demonstrated through the analysis of real data previously published.
conclusionSigReannot uses the oligo-nucleotide design procedure criteria to validate the probe-gene link and the Ensembl transcripts as reference for annotation. It therefore produces a high quality annotation based on reference gene sets.
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.