ArticleBMC proceedings2009
Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis.
Article in BMC proceedings, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 3 of them syntheses that pooled it.
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
76 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Pooled it
- Meta-analysis of molecular response of kidney to ischemia reperfusion injury for the identification of new candidate genes.BMC nephrology · 2013Pooled it
- Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.PLoS genetics · 2012Pooled it
- A Narrative Review on Integrative Bioinformatics Approaches for microRNA Research in Familial Mediterranean Fever: Current Insights and Future Directions.Health science reports · 2026Article
- Dysregulated mitochondrial energy metabolism drives the progression of mucosal field effects to invasive bladder cancer.The Journal of pathology · 2025Article
- Genome-wide RNA-Seq identifies TP53-mediated embryonic stem cells inhibiting tumor invasion and metastasis.Stem cell research & therapy · 2024Article
- Alterations in sperm RNAs persist after alcohol cessation and correlate with epididymal mitochondrial dysfunction.Andrology · 2024Article
- Transcriptome changes in the nucleus of the solitary tract induced by repeated stress, alcohol dependence, or stress-induced drinking in dependent mice.Neuropharmacology · 2024Article
- Preconception paternal alcohol exposure decreases IVF embryo survival and pregnancy success rates in a mouse model.Molecular human reproduction · 2023Article
- The origin of bladder cancer from mucosal field effects.iScience · 2022Article
- Integrative analysis to explore the biological association between environmental skin diseases and ambient particulate matter.Scientific reports · 2022Article
- Construction of a lncRNA-mRNA Co-Expression Network for Nasopharyngeal Carcinoma.Frontiers in oncology · 2022Article
- Maternal background alters the penetrance of growth phenotypes and sex-specific placental adaptation of offspring sired by alcohol-exposed males.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2021Article
- Gestational Exposure to Ultrafine Particles Reveals Sex- and Dose-Specific Changes in Offspring Birth Outcomes, Placental Morphology, and Gene Networks.Toxicological sciences : an official journal of the Society of Toxicology · 2021Article
- Programmed suppression of oxidative phosphorylation and mitochondrial function by gestational alcohol exposure correlate with widespread increases in H3K9me2 that do not suppress transcription.Epigenetics & chromatin · 2021Article
- Integrated Proteomic and Metabolomic Analysis of the Testes Characterizes BDE-47-Induced Reproductive Toxicity in Mice.Biomolecules · 2021Article
- Genetic analysis in European ancestry individuals identifies 517 loci associated with liver enzymes.Nature communications · 2021Article
- SARS-CoV-2 early infection signature identified potential key infection mechanisms and drug targets.BMC genomics · 2021Article
- Chemopreventive Property of Sencha Tea Extracts towards Sensitive and Multidrug-Resistant Leukemia and Multiple Myeloma Cells.Biomolecules · 2020Article
- RNA sequencing of corneas from two keratoconus patient groups identifies potential biomarkers and decreased NRF2-antioxidant responses.Scientific reports · 2020Article
16 more citing papers are in PubMed but not listed here.
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
backgroundOnce a list of differentially expressed genes has been identified from a microarray experiment, a subsequent post-analysis task is required in order to find the main biological processes associated to the experimental system. This paper describes two pathways analysis tools, ArrayUnlock and Ingenuity Pathways Analysis (IPA) to deal with the post-analyses of microarray data, in the context of the EADGENE and SABRE post-analysis workshop. Dataset employed in this study proceeded from an experimental chicken infection performed to study the host reactions after a homologous or heterologous secondary challenge with two species of Eimeria.
resultsAnalysis of the same microarray data source employing both commercial pathway analysis tools in parallel let to identify several biological and/or molecular functions altered in the chicken Eimeria maxima infection model, including several immune system related pathways. Biological functions differentially altered in the homologous and heterologous second infection were identified. Similarly, the effect of the timing in a homologous second infection was characterized by several biological functions.
conclusionFunctional analysis with ArrayUnlock and IPA provided information related to functional differences with the three comparisons of the chicken infection leading to similar conclusions. ArrayUnlock let an improvement of the annotations of the chicken genome adding InterPro annotations to the data set file. IPA provides two powerful tools to understand the pathway analysis results: the networks and canonical pathways that showed several pathways related to an adaptative immune response.
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.