ArticleMethods in molecular biology (Clifton, N.J.)2013
Building models using Reactome pathways as templates.
Article in Methods in molecular biology (Clifton, N.J.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- Label-Free Quantitative Proteomics in a Methylmalonyl-CoA Mutase-Silenced Neuroblastoma Cell Line.International journal of molecular sciences · 2018Article
- Article
- Combining membrane proteomics and computational three-way pathway analysis revealed signalling pathways preferentially regulated in human iPSCs and human ESCs.Scientific reports · 2017Article
- A novel approach to select differential pathways associated with hypertrophic cardiomyopathy based on gene co‑expression analysis.Molecular medicine reports · 2017Article
- Genome-wide identification of direct HBx genomic targets.BMC genomics · 2017Article
- In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis.PloS one · 2017Article
- Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer.Genome medicine · 2016Article
- Reactome from a WikiPathways Perspective.PLoS computational biology · 2016Article
- PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.Nucleic acids research · 2016Article
- Gramene 2016: comparative plant genomics and pathway resources.Nucleic acids research · 2016Article
- Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.BMC bioinformatics · 2015Article
- Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets.BMC genomics · 2015Article
- Mimoza: web-based semantic zooming and navigation in metabolic networks.BMC systems biology · 2015Article
- Dynamical modeling of uncertain interaction-based genomic networks.BMC bioinformatics · 2015Article
- Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges.Database : the journal of biological databases and curation · 2015Review
- GeneStoryTeller: a mobile app for quick and comprehensive information retrieval of human genes.Database : the journal of biological databases and curation · 2015Article
- Radiosensitization of human leukemic HL-60 cells by ATR kinase inhibitor (VE-821): phosphoproteomic analysis.International journal of molecular sciences · 2014Article
- Article
- Quantitative proteomics by SWATH-MS reveals altered expression of nucleic acid binding and regulatory proteins in HIV-1-infected macrophages.Journal of proteome research · 2014Article
- Gramene 2013: comparative plant genomics resources.Nucleic acids research · 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
1 author.
Funding
Abstract
The first steps of building a new model can be very time-consuming, involving consulting many research papers and then assembling a plausible network of reactions. In this chapter, tools for speeding up this process will be discussed. Reactome is a database containing extensive coverage of pathways in Homo sapiens and numerous reference species. It offers researchers wishing to create new models from scratch various tools for extracting the relevant reactions, complete with layout information. In this chapter, two use cases will be described, in which a modeller provides certain essential pieces of information and Reactome automatically constructs the basic models and then dumps them in SBML-ML format.
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.