ArticlePlant physiology2002
Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization.
Article in Plant physiology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed, 107 citations in OpenAlex.
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- 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
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- Meta Analysis of Gene Expression Data within and Across Species.Current genomics · 2008Article
- Rapid EST isolation from chromosome 1R of rye.BMC plant biology · 2008Article
- Isolation and characterization of expressed sequence tags (ESTs) from subtracted cDNA libraries of Pennisetum glaucum seedlings.Plant molecular biology · 2007Article
- Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.Genome research · 2007Article
- A microarray analysis of gene expression in the free-living stages of the parasitic nematode Strongyloides ratti.BMC genomics · 2006Article
- Changes in gene expression in maize kernel in response to water and salt stress.Plant cell reports · 2006Article
- Gene expression profiling in rice young panicle and vegetative organs and identification of panicle-specific genes through known gene functions.Molecular genetics and genomics : MGG · 2005Article
- Comparative analysis of expressed sequence tags from different organs of Vitis vinifera L.Functional & integrative genomics · 2005Article
- Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts.Plant physiology · 2005Article
- Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts.BMC genomics · 2005Article
- Endosperm-preferred expression of maize genes as revealed by transcriptome-wide analysis of expressed sequence tags.Plant molecular biology · 2005Article
- Identification by suppression subtractive hybridization of genes that are differentially expressed between near-isogenic maize lines in association with sugarcane mosaic virus resistance.Molecular genetics and genomics : MGG · 2005Article
- Profile and analysis of gene expression changes during early development in germinating spores of Ceratopteris richardii.Plant physiology · 2005Article
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Assembly of 73,000 expressed sequence tags (ESTs) representing multiple organs and developmental stages of maize (Zea mays) identified approximately 22,000 tentative unique genes (TUGs) at the criterion of 95% identity. Based on sequence similarity, overlap between any two of nine libraries with more than 3,000 ESTs ranged from 4% to 20% of the constituent TUGs. The most abundant ESTs were recovered from only one or a minority of the libraries, and only 26 EST contigs had members from all nine EST sets (presumably representing ubiquitously expressed genes). For several examples, ESTs for different members of gene families were detected in distinct organs. To study this further, two types of micro-array slides were fabricated, one containing 5,534 ESTs from 10- to 14-d-old endosperm, and the other 4,844 ESTs from immature ear, estimated to represent about 2,800 and 2,500 unique genes, respectively. Each array type was hybridized with fluorescent cDNA targets prepared from endosperm and immature ear poly(A(+)) RNA. Although the 10- to 14-d-old postpollination endosperm TUGs showed only 12% overlap with immature ear TUGs, endosperm target hybridized with 94% of the ear TUGs, and ear target hybridized with 57% of the endosperm TUGs. Incomplete EST sampling of low-abundance transcripts contributes to an underestimate of shared gene expression profiles. Reassembly of ESTs at the criterion of 90% identity suggests how cross hybridization among gene family members can overestimate the overlap in genes expressed in micro-array hybridization experiments.
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