ArticleNucleic acids research2009
Pomelo II: finding differentially expressed genes.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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.
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
30 citing papers in PubMed.
- Cytokine Antibody Microarray-Based Proteomic Strategies for Characterizing the Dysregulation of Cytokines Disease-Specific.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Protein Microarray Analysis with GenePix.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Transcriptomic analysis revealed potential regulatory biomarkers and repurposable drugs for breast cancer treatment.Cancer reports (Hoboken, N.J.) · 2024Article
- An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells.Nature communications · 2023Article
- Sulindac sulfide as a non-immune suppressive γ-secretase modulator to target triple-negative breast cancer.Frontiers in immunology · 2023Article
- Integrating Genomic Information with Tumor-Immune Microenvironment in Triple-Negative Breast Cancer.International journal of environmental research and public health · 2022Article
- Comprehensive molecular analysis of immortalization hallmarks in thyroid cancer reveals new prognostic markers.Clinical and translational medicine · 2022Article
- Analysis of Protein-Protein Interactions by Protein Microarrays.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Phage Microarrays for Screening of Humoral Immune Responses.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Recurrent Germline DLST Mutations in Individuals with Multiple Pheochromocytomas and Paragangliomas.American journal of human genetics · 2019Article
- An Integrative Genomics Approach for Associating Genetic Susceptibility with the Tumor Immune Microenvironment in Triple Negative Breast Cancer.Biomedical journal of scientific & technical research · 2019Article
- Gain-of-function mutations in DNMT3A in patients with paraganglioma.Genetics in medicine : official journal of the American College of Medical Genetics · 2018Article
- Whole Genome Transcriptome Analysis of the Association between Obesity and Triple-Negative Breast Cancer in Caucasian Women.International journal of environmental research and public health · 2018Article
- An Integrative Genomics Approach for Associating Genome-Wide Association Studies Information With Localized and Metastatic Prostate Cancer Phenotypes.Biomarker insights · 2017Article
- Integrative Analysis of MicroRNA-Mediated Gene Signatures and Pathways Modulating White Blood Cell Count in Childhood Acute Lymphoblastic Leukemia.Biomarker insights · 2017Article
- Molecular Analysis of Central Nervous System Disease Spectrum in Childhood Acute Lymphoblastic Leukemia.Clinical Medicine Insights. Oncology · 2016Article
- ABCG2 is a potential marker of tumor-initiating cells in breast cancer.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2015Article
- miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors.Genomics data · 2015Article
- Prognostic biomarkers for HNSCC using quantitative real-time PCR and microarray analysis: β-tubulin isotypes and the p53 interactome.Cytoskeleton (Hoboken, N.J.) · 2014Article
- Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness.Molecular & cellular proteomics : MCP · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pomelo II (http://pomelo2.bioinfo.cnio.es) is an open-source, web-based, freely available tool for the analysis of gene (and protein) expression and tissue array data. Pomelo II implements: permutation-based tests for class comparisons (t-test, ANOVA) and regression; survival analysis using Cox model; contingency table analysis with Fisher's exact test; linear models (of which t-test and ANOVA are especial cases) that allow additional covariates for complex experimental designs and use empirical Bayes moderated statistics. Permutation-based and Cox model analysis use parallel computing, which permits taking advantage of multicore CPUs and computing clusters. Access to, and further analysis of, additional biological information and annotations (PubMed references, Gene Ontology terms, KEGG and Reactome pathways) are available either for individual genes (from clickable links in tables and figures) or sets of genes. The source code is available, allowing for extending and reusing the software. A comprehensive test suite is also available, and covers both the user interface and the numerical results. The possibility of including additional covariates, parallelization of computation, open-source availability of the code and comprehensive testing suite make Pomelo II a unique tool.
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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.