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DATA ANALYSIS EXPRESSION MICROARRAYS

(Mostly for Affymetrix arrays)

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1. COMPARATIVE ANALYSIS OF MULTIPLE STATES

Description: Search and identification of significant genes using statistical techniques, 2-state differential contrast (NORMAL versus ALTERED) with a minimum of 2 biological replicates for each state. (To analyze fewer samples, see 3. CUSTOM ANALYSIS).

User Data: For the analysis the user must provide the raw data from each microarray (ie, the .CEL and .RPT).

Delivered Data (after analysis): Full report (PDF format .PDF) and data (Excel format .XLS) with a list of significant genes including the gene identifiers, the parameters of significance (p-values, adjusted p-values for multiple tests, R-folds and error estimation FDR), the names and the description of each gene. Each gene list should include 2 groups: the genes that are overexpressed (red) and the genes that are repressed (green), both compared with the controls.

Fees: Usually a 20% of the microarrays cost.

Request: Contact Diego Alonso at the Bioinformatics Unit: diego.alonso[at]usal.es

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2.GENE EXPRESSION PROFILES

Description: Analysis to identify the expression profile of selected genes of particular interest in all samples of a given set.

User Data: For the analysis the user must provide the raw data from each microarray (ie, the .CEL and .RPT).

Delivered Data: Full Report (PDF format) including figures of expression profiles.

Fees and Request: Contact Diego Alonso at the Bioinformatics Unit: diego.alonso[at]usal.es

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3. CUSTOM ANALYSIS

Description: Specific custom analysis or further studies on previous services.

Fees and Request: Contact Diego Alonso at the Bioinformatics Unit: diego.alonso[at]usal.es

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4. FUNCTIONAL ANALYSIS

Description: After identification of significant genes studies of biologically functional assignment can be carried out. This type of analyses are broad and can differ greatly depending on the objectives of each study. The Bioinformatics Unit provides support to researchers using several  functional analysis tools as well as help for the use of the Ingenuity program IPA.

Fees and Request: Contact Diego Alonso at the Bioinformatics Unit: diego.alonso[at]usal.es

As help and guidance for functional studies we included a page with information and links of several bioinformatics tools:


FUNCTIONAL ANALYSIS

 
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