ArticleBMC bioinformatics2012
Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 155 papers, 3 of them syntheses 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
155 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Meta-analysis of human prefrontal cortex reveals activation of GFAP and decline of synaptic transmission in the aging brain.Acta neuropathologica communications · 2020Pooled it
- Identification of LINC01279 as a cell cycle‑associated long non‑coding RNA in endometriosis with GBA analysis.Molecular medicine reports · 2018Pooled it
- Meta-analysis of gene expression in relapsed childhood B-acute lymphoblastic leukemia.BMC cancer · 2017Pooled it
- ISA101 and nivolumab for HPV-16Journal for immunotherapy of cancer · 2022Trial
- TMC6 Protects Against Ischemic Neuronal Injury by Activating Rap1/Rac1 Signaling to Restore Mitochondrial Dynamics and Mitophagy.Molecular neurobiology · 2026Article
- Data normalization and reanalysis of the pruritus-associated genes from microarray analysis.Journal of the European Academy of Dermatology and Venereology : JEADV · 2026Article
- STC2-mediated calcium homeostasis dysregulation in the osteosarcoma microenvironment: Insights from single-cell sequencing and machine learning.Translational oncology · 2026Article
- Glioma biomarker analysis and drug targeting prediction based on ferroptosis-related genes.Medicine · 2026Article
- Multi-omics data mining combined with experimental validation reveals ferroptosis- and autophagy-associated hub genes as diagnostic candidates and immune modulators in atherosclerosis.Animal models and experimental medicine · 2026Article
- Cardamonin ameliorates neuroinflammation in Parkinson's disease by regulating NF-κB signaling.Hereditas · 2026Article
- Folic Acid Targeting Shared Sepsis-Osteoporosis Pathogenesis: From Computational Discovery to Dynamic Binding Mechanisms.ACS omega · 2026Article
- FGFR2 is a Candidate Immune-Associated Marker of Diabetic Foot Ulcer That Promotes Keratinocyte Function by Activating the PI3K/Akt and MAPK Pathways.Mediators of inflammation · 2026Article
- Construction and validation of a novel diagnostic model for esophageal squamous cell carcinoma: an integrated analysis of multi-omics data.Frontiers in immunology · 2026Article
- Combining mitochondrial proteomes and Mendelian randomization to identify novel therapeutic targets for diabetic nephropathy.Renal failure · 2025Article
- Decoding Potential Cuproptosis-Related Genes in Sarcopenia: A Multi-Omics Network Analysis.Biology · 2025Article
- Exploration of genes associated with cellular senescence in lung ischemia-reperfusion injury and connection to immune infiltration.Clinical and experimental medicine · 2025Article
- IRS2/FOXO1 mitigates osteoarthritis by regulating chondrocyte autophagy and mitochondrial function.Molecular medicine (Cambridge, Mass.) · 2025Article
- MelanoDB: A dataset of clinical and molecular features of patients with advanced melanoma treated with MAPK inhibitors.Scientific data · 2025Article
- PXMP2 inhibits tumor stemness and immune infiltration in hepatocellular carcinoma based on stemness risk.Discover oncology · 2025Article
- Integrative bioinformatics analysis of lipid metabolism-related genes and immune infiltration in endometriosis.Medicine · 2025Article
95 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
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWith an abundant amount of microarray gene expression data sets available through public repositories, new possibilities lie in combining multiple existing data sets. In this new context, analysis itself is no longer the problem, but retrieving and consistently integrating all this data before delivering it to the wide variety of existing analysis tools becomes the new bottleneck.
resultsWe present the newly released inSilicoMerging R/Bioconductor package which, together with the earlier released inSilicoDb R/Bioconductor package, allows consistent retrieval, integration and analysis of publicly available microarray gene expression data sets. Inside the inSilicoMerging package a set of five visual and six quantitative validation measures are available as well.
conclusionsBy providing (i) access to uniformly curated and preprocessed data, (ii) a collection of techniques to remove the batch effects between data sets from different sources, and (iii) several validation tools enabling the inspection of the integration process, these packages enable researchers to fully explore the potential of combining gene expression data for downstream analysis. The power of using both packages is demonstrated by programmatically retrieving and integrating gene expression studies from the InSilico DB repository [https://insilicodb.org/app/].
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.