ArticleComparative and functional genomics2004
TRANSPATH--a high quality database focused on signal transduction.
Article in Comparative and functional genomics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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
17 citing papers in PubMed, 35 citations in OpenAlex.
- Comparative analysis of deeply phenotyped GBM cohorts of 'short-term' and 'long-term' survivors.Journal of neuro-oncology · 2023Article
- Text mining-based word representations for biomedical data analysis and protein-protein interaction networks in machine learning tasks.PloS one · 2021Article
- Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources.Briefings in bioinformatics · 2019Review
- Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data.EuPA open proteomics · 2016Article
- Protein function in precision medicine: deep understanding with machine learning.FEBS letters · 2016Review
- Lynx: a knowledge base and an analytical workbench for integrative medicine.Nucleic acids research · 2016Article
- Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism.BMC systems biology · 2014Article
- Lynx: a database and knowledge extraction engine for integrative medicine.Nucleic acids research · 2014Article
- Dynamics and structure in cell signaling networks: off-state stability and dynamically positive cycles.PloS one · 2013Article
- Inhibition of glycolytic enzymes mediated by pharmacologically activated p53: targeting Warburg effect to fight cancer.The Journal of biological chemistry · 2011Article
- Modeling and analysis of retinoic acid induced differentiation of uncommitted precursor cells.Integrative biology : quantitative biosciences from nano to macro · 2011Article
- Patterns of human gene expression variance show strong associations with signaling network hierarchy.BMC systems biology · 2010Article
- Molecular mechanistic associations of human diseases.BMC systems biology · 2010Article
- Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data.PLoS computational biology · 2010Article
- Article
- PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes.Nucleic acids research · 2009Article
- The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'.Comparative and functional genomics · 2004Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
TRANSPATH can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyser. Therefore, three modules have been created: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence faciliates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. More information is available at www.biobase.de/pages/products/databases.html.
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.