ArticleBMC bioinformatics2007
From genes to functional classes in the study of biological systems.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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68 citing papers in PubMed.
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- TDP-43 regulates cancer-associated microRNAs.Protein & cell · 2018Article
- Regulation of gene expression is associated with tolerance of the Arctic copepodEcology and evolution · 2017Article
- Mass spectrometry analysis and transcriptome sequencing reveal glowing squid crystal proteins are in the same superfamily as firefly luciferase.Scientific reports · 2016Article
- RNA sequencing reveals retinal transcriptome changes in STZ-induced diabetic rats.Molecular medicine reports · 2016Article
- Integrating transcriptomic and metabolomic analysis to understand natural leaf senescence in sunflower.Plant biotechnology journal · 2016Article
- Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis.Molecular metabolism · 2016Article
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- Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma.Clinical epigenetics · 2015Article
- Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework.BMC bioinformatics · 2014Article
- Understanding disease mechanisms with models of signaling pathway activities.BMC systems biology · 2014Article
- Programmed cell death activated by Rose Bengal in Arabidopsis thaliana cell suspension cultures requires functional chloroplasts.Journal of experimental botany · 2014Article
- Capturing the biological impact of CDKN2A and MC1R genes as an early predisposing event in melanoma and non melanoma skin cancer.Oncotarget · 2014Article
- Permanent cardiac sarcomere changes in a rabbit model of intrauterine growth restriction.PloS one · 2014Article
8 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
backgroundWith the popularization of high-throughput techniques, the need for procedures that help in the biological interpretation of results has increased enormously. Recently, new procedures inspired in systems biology criteria have started to be developed.
resultsHere we present FatiScan, a web-based program which implements a threshold-independent test for the functional interpretation of large-scale experiments that does not depend on the pre-selection of genes based on the multiple application of independent tests to each gene. The test implemented aims to directly test the behaviour of blocks of functionally related genes, instead of focusing on single genes. In addition, the test does not depend on the type of the data used for obtaining significance values, and consequently different types of biologically informative terms (gene ontology, pathways, functional motifs, transcription factor binding sites or regulatory sites from CisRed) can be applied to different classes of genome-scale studies. We exemplify its application in microarray gene expression, evolution and interactomics.
conclusionMethods for gene set enrichment which, in addition, are independent from the original data and experimental design constitute a promising alternative for the functional profiling of genome-scale experiments. A web server that performs the test described and other similar ones can be found at: http://www.babelomics.org.
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