Unknown,Transcriptomics,Genomics,Proteomics

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Arabidopsis at the stage of Golovinomyces cichoracearum haustorium formation

ABSTRACT: Here, we sought to describe qualitative and quantitative changes in the global gene expression profiles of susceptible Arabidopsis plants supporting the development of G. cichoracearum haustoria. We analyzed the features of compatibility at this infection stage, and further evaluated the contribution of the SA- and JA/ET-dependent defense signaling pathways in the pathogen-induced responses by comparing responses in infected wild-type, npr1-1, and jar1-1 plants. Our findings collectively contribute to knowledge regarding early host cell alterations generated in response to attack by this virulent obligate biotrophic fungus. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Disease State: plant infected/uninfected with Golovinomyces orontii Genotype: wt/mutant strains Keywords: Logical Set Computed

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Georgina Fabro

PROVIDER: E-GEOD-13199 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide expression profiling Arabidopsis at the stage of Golovinomyces cichoracearum haustorium formation.

Fabro Georgina G Di Rienzo Julio A JA Voigt Christian A CA Savchenko Tatyana T Dehesh Katayoon K Somerville Shauna S Alvarez María Elena ME

Plant physiology 20080124 3

Compatibility between plants and obligate biotrophic fungi requires fungal mechanisms for efficiently obtaining nutrients and counteracting plant defenses under conditions that are expected to induce changes in the host transcriptome. A key step in the proliferation of biotrophic fungi is haustorium differentiation. Here we analyzed global gene expression patterns in Arabidopsis thaliana leaves during the formation of haustoria by Golovinomyces cichoracearum. At this time, the endogenous levels ...[more]

PMID: 18218973

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Project description:Summary: Breast cancer cell lines have been used widely to investigate breast cancer pathobiology and new therapies. Breast cancer is a molecularly heterogeneous disease, and it is important to understand how well and which cell lines best model that diversity. In particular, microarray studies have identified molecular subtypes (luminal A, luminal B, ERBB2-associated, basal-like and normal-like) with characteristic gene-expression patterns and underlying DNA copy number alterations (CNAs). Here, we studied a collection of breast cancer cell lines to catalog molecular profiles and to assess their relation to breast cancer subtypes. Whole-genome DNA microarrays were used to profile gene expression and CNAs in a collection of 52 widely-used breast cancer cell lines, and comparisons were made to existing profiles of primary breast tumors. Hierarchical clustering was used to identify gene-expression subtypes, and Gene Set Enrichment Analysis (GSEA) to discover biological features of those subtypes. Genomic and transcriptional profiles were integrated to discover within high-amplitude CNAs candidate cancer genes with coordinately altered gene copy number and expression. Transcriptional profiling of breast cancer cell lines identified one luminal and two basal-like (A and B) subtypes. Luminal lines displayed an estrogen receptor (ER) signature and resembled luminal-A/B tumors, basal-A lines were associated with ETS-pathway and BRCA1 signatures and resembled basal-like tumors, and basal-B lines displayed mesenchymal and stem-cell characteristics. Compared to tumors, cell lines exhibited similar patterns of CNA, but an overall higher complexity of CNA (genetically simple luminal-A tumors were not represented), and only partial conservation of subtype-specific CNAs. We identified 80 high-level DNA amplifications and 13 presumptive homozygous deletions, and the resident genes with concomitantly altered gene-expression, highlighting known and novel candidate breast cancer genes. Overall, breast cancer cell lines were genetically more complex than tumors, but retained expression patterns with relevance to the luminal-basal subtype distinction. The compendium of molecular profiles defines cell lines suitable for investigations of subtype-specific pathobiology, biomarkers and therapies, and provides a resource for discovery of new breast cancer genes. HEEBO oligonucleotide microarrays from the Stanford Functional Genomics Facility were used to perform gene expression profiling of 50 human breast epithelial cell lines, in comparison to a universal RNA reference. Expression data were analyzed by hierarchical clustering to identify subgroups, and gene set enrichment analysis to identify subgroup-specific gene pathways.

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Dataset Information

Arabidopsis at the stage of Golovinomyces cichoracearum haustorium formation

Publications

Genome-wide expression profiling Arabidopsis at the stage of Golovinomyces cichoracearum haustorium formation.

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