ArticleNature protocols2010
Expander: from expression microarrays to networks and functions.
Article in Nature protocols, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
What it found
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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
123 citing papers in PubMed.
- Trial
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- MicroRNA signatures associated with radioiodine refractoriness and tumor dedifferentiation in metastatic papillary thyroid carcinoma.Endocrine · 2026Article
- Molecular and biochemical components associated with chilling tolerance in tomato: comparison of different developmental stages.Molecular horticulture · 2024Article
- Analysis of alpha-1-antitrypsin (AAT)-regulated, glucocorticoid receptor-dependent genes in macrophages reveals a novel host defense function of AAT.Physiological reports · 2024Article
- Biclustering data analysis: a comprehensive survey.Briefings in bioinformatics · 2024Review
- Profile of MicroRNAs Associated with Death Due to Disease Progression in Metastatic Papillary Thyroid Carcinoma Patients.Cancers · 2023Article
- The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration.PLoS biology · 2023Article
- Astrocyte immunometabolic regulation of the tumour microenvironment drives glioblastoma pathogenicity.Brain : a journal of neurology · 2022Article
- Genome-wide analysis of MYB transcription factors of Vaccinium corymbosum and their positive responses to drought stress.BMC genomics · 2021Article
- Guard cells control hypocotyl elongation through HXK1, HY5, and PIF4.Communications biology · 2021Article
- Transcriptomic analysis of cork during seasonal growth highlights regulatory and developmental processes from phellogen to phellem formation.Scientific reports · 2021Article
- Classification of node-positive melanomas into prognostic subgroups using keratin, immune, and melanogenesis expression patterns.Oncogene · 2021Article
- GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super-enhancers.Nature communications · 2021Article
- Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors.eLife · 2021Article
- Multiple genetic programs contribute to CD4 T cell memory differentiation and longevity by maintaining T cell quiescence.Cellular immunology · 2020Article
- Bile Ductal Transcriptome Identifies Key Pathways and Hub Genes in Clonorchis sinensis-Infected Sprague-Dawley Rats.The Korean journal of parasitology · 2020Article
- Global Evolutionary Analysis of 11 Gene Families Part of Reactive Oxygen Species (ROS) Gene Network in FourAntioxidants (Basel, Switzerland) · 2020Article
- QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data.Bioinformatics (Oxford, England) · 2020Article
63 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
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A major challenge in the analysis of gene expression microarray data is to extract meaningful biological knowledge out of the huge volume of raw data. Expander (EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use. It is designed to support all the stages of microarray data analysis, from raw data normalization to inference of transcriptional regulatory networks. The microarray analysis described in this protocol starts with importing the data into Expander 5.0 and is followed by normalization and filtering. Then, clustering and network-based analyses are performed. The gene groups identified are tested for enrichment in function (based on Gene Ontology), co-regulation (using transcription factor and microRNA target predictions) or co-location. The results of each analysis step can be visualized in a number of ways. The complete protocol can be executed in approximately 1 h.
Indexed as
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20134430What 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.