ArticleBMC bioinformatics2011
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed.
- Functional Genomics Approach Identifies Novel Signaling Regulators of TGFα Ectodomain Shedding.Molecular cancer research : MCR · 2018Article
- Overcoming the divide between ataxias and spastic paraplegias: Shared phenotypes, genes, and pathways.Movement disorders : official journal of the Movement Disorder Society · 2017Review
- Protein-protein interaction analysis for functional characterization of helicases.Methods (San Diego, Calif.) · 2016Review
- Whole-exome sequencing in obsessive-compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways.Translational psychiatry · 2016Article
- Characterization of protein complexes and subcomplexes in protein-protein interaction databases.Biochemistry research international · 2015Article
- Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development.Clinical and translational medicine · 2014Article
- Integrating in silico resources to map a signaling network.Methods in molecular biology (Clifton, N.J.) · 2014Article
- A survey of protein interaction data and multigenic inherited disorders.BMC bioinformatics · 2013Article
- Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction.BMC bioinformatics · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe iRefIndex consolidates protein interaction data from ten databases in a rigorous manner using sequence-based hash keys. Working with consolidated interaction data comes with distinct challenges: data are redundant, overlapping, highly interconnected and may be collected and represented using different curation practices. These phenomena were quantified in our previous studies.
resultsThe iRefScape plug-in for the Cytoscape graphical viewer addresses these challenges. We show how these factors impact on data-mining tasks and how our solutions resolve them in a simple and efficient manner. A uniform accession space is used to limit redundancy and support search expansion and searching on multiple accession types. Multiple node and edge features support data filtering and mining. Node colours and features supply information about search result provenance. Overlapping evidence is presented using a multi-graph and a bi-partite representation is used to distinguish binary and n-ary source data. Searching for interactions between sets of proteins is supported and specifically includes searches on disease-related genes found in OMIM. Finally, a synchronized adjacency-matrix view facilitates visualization of relationships between sets of user defined groups.
conclusionsThe iRefScape plug-in will be of interest to advanced users of interaction data. The plug-in provides access to a consolidated data set in a uniform accession space while remaining faithful to the underlying source data. Tools are provided to facilitate a range of tasks from a simple search to knowledge discovery. The plug-in uses a number of strategies that will be of interest to other plug-in developers.
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.