ArticleGenome research1999
Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression.
Article in Genome research, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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86 citing papers in PubMed.
- Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR.PeerJ · 2015Article
- Towards systems biological understanding of leaf senescence.Plant molecular biology · 2013Review
- Fine-tuning of microRNA-mediated repression of mRNA by splicing-regulated and highly repressive microRNA recognition element.BMC genomics · 2013Article
- Evaluation of genome sequencing quality in selected plant species using expressed sequence tags.PloS one · 2013Article
- Expressed sequence tags in cultivated peanut (Arachis hypogaea): discovery of genes in seed development and response to Ralstonia solanacearum challenge.Journal of plant research · 2012Article
- Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum).DNA research : an international journal for rapid publication of reports on genes and genomes · 2012Article
- Large-scale sequencing of normalized full-length cDNA library of soybean seed at different developmental stages and analysis of the gene expression profiles based on ESTs.Molecular biology reports · 2012Article
- Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidates.BMC genomics · 2012Article
- Differential gene expression and associated QTL mapping for cotton yield based on a cDNA-AFLP transcriptome map in an immortalized F2.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
- Infection of Arabidopsis thaliana by Phytophthora parasitica and identification of variation in host specificity.Molecular plant pathology · 2011Article
- Generation and analysis of ESTs from strawberry (Fragaria xananassa) fruits and evaluation of their utility in genetic and molecular studies.BMC genomics · 2010Article
- Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types.BMC genomics · 2010Article
- Prevalence of alternative splicing choices in Arabidopsis thaliana.BMC plant biology · 2010Article
- The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.).BMC plant biology · 2010Article
- Construction and application of an electronic spatiotemporal expression profile and gene ontology analysis platform based on the EST database of the silkworm, Bombyx mori.Journal of insect science (Online) · 2010Article
- Isolation and functional characterization of cold-regulated promoters, by digitally identifying peach fruit cold-induced genes from a large EST dataset.BMC plant biology · 2009Article
- Article
- Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing.BMC genomics · 2009Article
- Identification and functional validation of a unique set of drought induced genes preferentially expressed in response to gradual water stress in peanut.Molecular genetics and genomics : MGG · 2009Article
- Poaceae genomes: going from unattainable to becoming a model clade for comparative plant genomics.Plant physiology · 2009Article
26 more citing papers are in PubMed but not listed here.
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Large, publicly available collections of expressed sequence tags (ESTs) have been generated from Arabidopsis thaliana and rice (Oryza sativa). A potential, but relatively unexplored application of this data is in the study of plant gene expression. Other EST data, mainly from human and mouse, have been successfully used to point out genes exhibiting tissue- or disease-specific expression, as well as for identification of alternative transcripts. In this report, we go a step further in showing that computer analyses of plant EST data can be used to generate evidence of correlated expression patterns of genes across various tissues. Furthermore, tissue types and organs can be classified with respect to one another on the basis of their global gene expression patterns. As in previous studies, expression profiles are first estimated from EST counts. By clustering gene expression profiles or whole cDNA library profiles, we show that genes with similar functions, or cDNA libraries expected to share patterns of gene expression, are grouped together. Promising uses of this technique include functional genomics, in which evidence of correlated expression might complement (or substitute for) those of sequence similarity in the annotation of anonymous genes and identification of surrogate markers. The analysis presented here combines the application of a correlation-based clustering method with a graphical color map allowing intuitive visualization of patterns within a large table of expression measurements.
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