Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Whole reference dataset (cell wall chip)

ABSTRACT: Data processing included: 1. Filtering of those bad quality image spots (these includes alterations on the shape or hybridization) 2. Filtering of low intensity which was done flagging with -50 those spots whose feature intensity was lower in any of both channels than the average of the local background in the corresponding channel for all spots. However, those genes whose feature intensity in one channel was under the limit but in the other channel was 5 times over limit were considered as on-off genes and were not filtered. 3. Filtering of low reproducibility intrachip replicated spots. Normal distribution was created with the value obtained from the formula: log2(Rax1/Rb) which means logarithm (two-based) of one ratio multiplied by the inverse of its replicate. This value for each gene shoud keep between the range of average Â± 3SD. Those genes out of these range are flagged as -25 4. Normalization of ratios was done by Lowess mathematical method. Correction factor was 0.33

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Rosa PÃ©rez-DÃaz

PROVIDER: E-GEOD-2105 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The 'yeast cell wall chip' - a tool to analyse the regulation of cell wall biogenesis in Saccharomyces cerevisiae.

Rodríguez-Peña Jose M JM Pérez-Díaz Rosa M RM Alvarez Sara S Bermejo Clara C García Raúl R Santiago Catalina C Nombela César C Arroyo Javier J

Microbiology (Reading, England) 20050701 Pt 7

Within the field of Saccharomyces cerevisiae functional genomics, DNA microarrays have become a very useful tool to study genome-wide gene-expression changes under diverse experimental conditions. Here, the design and production of a gene microarray, called the 'yeast cell wall chip', specifically tailored to investigate cell wall functions, is described. This array has been validated and shown to be useful to address gene involvement in the regulation of the response to cell wall damage in yeas ...[more]

PMID: 16000714

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Dataset Information

Whole reference dataset (cell wall chip)

Publications

The 'yeast cell wall chip' - a tool to analyse the regulation of cell wall biogenesis in Saccharomyces cerevisiae.

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