ArticleProceedings. IEEE International Conference on Bioinformatics and Biomedicine2011
Systems Approach to Identifying Relevant Pathways from Phenotype Information in Dose-Dependent Time Series Microarray Data.
Article in Proceedings. IEEE International Conference on Bioinformatics and Biomedicine, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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.
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Who cites it
6 citing papers in PubMed, 8 citations in OpenAlex.
- Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials.Scientific data · 2021Article
- mRNA and miRNA regulatory networks reflective of multi-walled carbon nanotube-induced lung inflammatory and fibrotic pathologies in mice.Toxicological sciences : an official journal of the Society of Toxicology · 2015Article
- System-based identification of toxicity pathways associated with multi-walled carbon nanotube-induced pathological responses.Toxicology and applied pharmacology · 2013Article
- New perspectives for in vitro risk assessment of multiwalled carbon nanotubes: application of coculture and bioinformatics.Journal of toxicology and environmental health. Part B, Critical reviews · 2012Article
- Integrated miRNA and mRNA Analysis of Time Series Microarray Data.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and BiomedicineArticle
- Similar and Differential Canonical Pathways and Biological Processes Associated With Multiwalled Carbon Nanotube and Asbestos-Induced Pulmonary Fibrosis: A 1-Year Postexposure Study.International journal of toxicologyArticle
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
This study presents a novel computational approach to find relevant pathways from dose-dependent time series gene expression data which are significantly associated with a phenotype pattern pathological patterns in the comprehensive evaluation of database of pathways. Our system uses four steps: 1) identify a set of genes which change significantly in dose or time; 2) find phenotype patterns and gene coefficients for the genes found in step 1; 3) expand to genome-wide coefficients, and 4) identify pathways which are significantly relevant to a phenotype pattern. Our technique finds biologically relevant pathways with and without phenotype-constraints. Our system has been used on genome-wide expression profiles of mouse lungs (n=160) following aspiration of well dispersed multi-walled carbon nanotubes (MWCNT), in order to detect MWCNT-induced lung inflammation and related pathways. The identified significant pathways are supported by evidence in the literature and biological validation.
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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.