ArticleNucleic acids research2005
Linking disease-associated genes to regulatory networks via promoter organization.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation.BMC genomics · 2008Pooled it
- SEQSIM: A novel bioinformatics tool for comparisons of promoter regions-a case study of calcium binding protein spermatid associated 1 (CABS1).BMC bioinformatics · 2025Article
- An enhanced BERT model with improved local feature extraction and long-range dependency capture in promoter prediction for hearing loss.PeerJ. Computer science · 2025Article
- iPro2L-DG: Hybrid network based on improved densenet and global attention mechanism for identifying promoter sequences.Heliyon · 2024Article
- Article
- Transcriptional regulation of prolactin in a euryhaline teleost: Characterisation of gene promoters through in silico and transcriptome analyses.Journal of neuroendocrinology · 2020Review
- Classifying Promoters by Interpreting the Hidden Information of DNA Sequences via Deep Learning and Combination of Continuous FastText N-Grams.Frontiers in bioengineering and biotechnology · 2019Article
- Function Over Form: Modeling Groups of Inherited Neurological Conditions in Zebrafish.Frontiers in molecular neuroscience · 2016Review
- Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks.PLoS computational biology · 2015Article
- Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection.Nucleic acids research · 2012Article
- Linkage of cardiac gene expression profiles and ETS2 with lifespan variability in rats.Aging cell · 2012Article
- Bioinformatics identification of modules of transcription factor binding sites in Alzheimer's disease-related genes by in silico promoter analysis and microarrays.International journal of Alzheimer's disease · 2011Article
- BiologicalNetworks 2.0--an integrative view of genome biology data.BMC bioinformatics · 2010Article
- A molecular profile of focal segmental glomerulosclerosis from formalin-fixed, paraffin-embedded tissue.The American journal of pathology · 2010Article
- Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.Nucleic acids research · 2010Article
- Networking of differentially expressed genes in human cancer cells resistant to methotrexate.Genome medicine · 2009Article
- Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis.BMC bioinformatics · 2009Article
- In silico promoters: modelling of cis-regulatory context facilitates target predictio.Journal of cellular and molecular medicine · 2009Review
- SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency.PloS one · 2008Article
- In Silico Promoter Analysis can Predict Genes of Functional Relevance in Cell Proliferation: Validation in a Colon Cancer Model.Translational oncogenomics · 2007Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pathway- or disease-associated genes may participate in more than one transcriptional co-regulation network. Such gene groups can be readily obtained by literature analysis or by high-throughput techniques such as microarrays or protein-interaction mapping. We developed a strategy that defines regulatory networks by in silico promoter analysis, finding potentially co-regulated subgroups without a priori knowledge. Pairs of transcription factor binding sites conserved in orthologous genes (vertically) as well as in promoter sequences of co-regulated genes (horizontally) were used as seeds for the development of promoter models representing potential co-regulation. This approach was applied to a Maturity Onset Diabetes of the Young (MODY)-associated gene list, which yielded two models connecting functionally interacting genes within MODY-related insulin/glucose signaling pathways. Additional genes functionally connected to our initial gene list were identified by database searches with these promoter models. Thus, data-driven in silico promoter analysis allowed integrating molecular mechanisms with biological functions of the cell.
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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.