Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression of Annotated Genes

ABSTRACT: Contains a row for each annotated gene in each sample, indicating whether our analysis called the gene "present" or "absent" in the sample. Gene names and coordinates refer to version 3 of the TIGR annotation as submitted to GenBank (GI numbers 22330780, 22326553, 22331929, 22329272, 22328163).

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Rosa Cheuk

PROVIDER: E-GEOD-636 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Empirical analysis of transcriptional activity in the Arabidopsis genome.

Yamada Kayoko K Lim Jun J Dale Joseph M JM Chen Huaming H Shinn Paul P Palm Curtis J CJ Southwick Audrey M AM Wu Hank C HC Kim Christopher C Nguyen Michelle M Pham Paul P Cheuk Rosa R Karlin-Newmann George G Liu Shirley X SX Lam Bao B Sakano Hitomi H Wu Troy T Yu Guixia G Miranda Molly M Quach Hong L HL Tripp Matthew M Chang Charlie H CH Lee Jeong M JM Toriumi Mitsue M Chan Marie M H MM Tang Carolyn C CC Onodera Courtney S CS Deng Justine M JM Akiyama Kenji K Ansari Yasser Y Arakawa Takahiro T Banh Jenny J Banno Fumika F Bowser Leah L Brooks Shelise S Carninci Piero P Chao Qimin Q Choy Nathan N Enju Akiko A Goldsmith Andrew D AD Gurjal Mani M Hansen Nancy F NF Hayashizaki Yoshihide Y Johnson-Hopson Chanda C Hsuan Vickie W VW Iida Kei K Karnes Meagan M Khan Shehnaz S Koesema Eric E Ishida Junko J Jiang Paul X PX Jones Ted T Kawai Jun J Kamiya Asako A Meyers Cristina C Nakajima Maiko M Narusaka Mari M Seki Motoaki M Sakurai Tetsuya T Satou Masakazu M Tamse Racquel R Vaysberg Maria M Wallender Erika K EK Wong Cecilia C Yamamura Yuki Y Yuan Shiaulou S Shinozaki Kazuo K Davis Ronald W RW Theologis Athanasios A Ecker Joseph R JR

Science (New York, N.Y.) 20031001 5646

Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel t ...[more]

PMID: 14593172

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Project description:Changes in human bladder epithelial cell gene expression associated with interstitial cystitis or antiproliferative factor treatment. Explanted bladder epithelial cells from patients with interstitial cystitis (IC) have been shown to differ from explanted control cells in several ways, including production of an antiproliferative factor (APF), altered production of certain epithelial growth factors, and rate of proliferation. To better understand the role of the APF in abnormal bladder epithelial cell proliferation in IC, we studied gene expression patterns in normal bladder epithelial cells treated with APF vs. mock APF and compared them to expression patterns in IC vs. normal cells using microarray analysis. Oligo-dT-primed total cellular RNA was labeled with [33P]dCTP and hybridized to GeneFilter GF211 microarray membranes (Research Genetics) containing cDNA for 3,964 human genes. Thirteen genes that function in epithelial cell proliferation or differentiation were consistently differentially expressed in both IC (compared with control) and APF-treated (compared with mock APF-treated) normal bladder epithelial cells. The general pattern of gene expression in IC and APF-treated cells suggested a less proliferative phenotype, with increased expression of E-cadherin, phosphoribosylpyrophosphate synthetase-associated protein 39, and SWI/SNF complex 170-kDa subunit, and decreased expression of vimentin, {alpha}2-integrin, {alpha}1-catenin, cyclin D1, and jun N-terminal kinase 1; these findings were confirmed for the structural gene products (E-cadherin, vimentin, {alpha}2-integrin, and {alpha}-catenin) by immunohistochemistry. These results are compatible with the previously noted decreased proliferation rate of IC and APF-treated normal cells, and indicate that the mechanism whereby APF inhibits cell proliferation may involve both downregulation of genes that stimulate cell proliferation along with upregulation of genes that inhibit cell growth.

Dataset Information

Expression of Annotated Genes

Publications

Empirical analysis of transcriptional activity in the Arabidopsis genome.

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