ArticleNucleic acids research2010
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 232 papers, 5 of them syntheses that pooled it.
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Who cites it
232 citing papers in PubMed, 5 syntheses or guidelines pooled it.
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- The Interplay of Microtubules with Mitochondria-ER Contact Sites (MERCs) in Glioblastoma.Biomolecules · 2022Pooled it
- Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker.Nucleic acids research · 2017Pooled it
- Pooled it
- A quantitative transcriptome reference map of the normal human brain.Neurogenetics · 2014Pooled it
- Single-cell and spatial omics reveals region-specific plasticity and therapeutic vulnerabilities in metastatic high-risk neuroblastoma.Science advances · 2026Article
- RBM20 isoform regulation by independent transcription start sites adapts alternative splicing in development and disease.Nature communications · 2026Article
- Multi-Compartment Transcriptomics Identifies a Persistent Inflammatory Program and a Network-Derived Diagnostic Signature in Polycythemia Vera.International journal of molecular sciences · 2026Article
- P300/CBP inhibition with inobrodib in combination with gilteritinib and venetoclax targets leukemia stem cells in epigenetic mutant AML.Science advances · 2026Article
- FOXM1 inhibitor, RCM‑1, enhances venetoclax mediated apoptosis through downregulation of ATP2B4 in rhabdomyosarcoma.International journal of oncology · 2026Article
- Disruption of androgen receptor-cofactor interactions by the RNA-binding protein FUS/TLS alters androgen signalling in prostate cancer.Oncogene · 2026Article
- CoREST complex inhibition alters RNA splicing to promote neoantigen expression and enhance tumor immunity.JCI insight · 2026Article
- Proteoglycan-4 potentiates the antitumor efficacy of regorafenib in an orthotopic model of hepatocellular carcinoma.Journal of experimental & clinical cancer research : CR · 2025Article
- TLR2 agonism suppresses myeloid leukemogenesis by reprogramming leukemia stem cells.Blood advances · 2025Article
- Unraveling the impact of crizotinib to promote megakaryopoiesis for alleviating thrombocytopenia in myelodysplastic neoplasms.Leukemia · 2025Article
- The nonsteroidal anti-inflammatory drug sulindac reverses obesity-driven immunosuppression and triple-negative breast cancer progression.Breast cancer research : BCR · 2025Article
- Single-cell and Spatial Omics Reveals Region-Specific Plasticity and Therapeutic Vulnerabilities in Metastatic High-Risk Neuroblastoma.bioRxiv : the preprint server for biology · 2025Article
- Dek Loss Induces Sex-Dependent, Task-Specific Cognitive Deficits and Reprograms the Hippocampal Transcriptome in Mice.Research square · 2025Article
- Simultaneous inhibition of TRIM24 and TRIM28 sensitises prostate cancer cells to antiandrogen therapy, decreasing VEGF signalling and angiogenesis.Molecular oncology · 2025Article
- Article
172 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Alternative splicing is an important mechanism for increasing protein diversity. However, its functional effects are largely unknown. Here, we present our new software workflow composed of the open-source application AltAnalyze and the Cytoscape plugin DomainGraph. Both programs provide an intuitive and comprehensive end-to-end solution for the analysis and visualization of alternative splicing data from Affymetrix Exon and Gene Arrays at the level of proteins, domains, microRNA binding sites, molecular interactions and pathways. Our software tools include easy-to-use graphical user interfaces, rigorous statistical methods (FIRMA, MiDAS and DABG filtering) and do not require prior knowledge of exon array analysis or programming. They provide new methods for automatic interpretation and visualization of the effects of alternative exon inclusion on protein domain composition and microRNA binding sites. These data can be visualized together with affected pathways and gene or protein interaction networks, allowing a straightforward identification of potential biological effects due to alternative splicing at different levels of granularity. Our programs are available at http://www.altanalyze.org and http://www.domaingraph.de. These websites also include extensive documentation, tutorials and sample data.
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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.