GEPAS and Babelomics. Ignacio Medina David Montaner Bioinformatics Department Functional Genomics Unit

Transcription

1 GEPAS and Babelomics Ignacio Medina David Montaner Bioinformatics Department Functional Genomics Unit

2 GEPAS/Babelomics Definitions GEPAS The Gene Expression Profile Analysis Suite is one of the most complete integrated packages of tools for microarray data analysis available over the web Babelomics Babelomics is a complete suite of web tools for functional analysis of genome scale experiments

3 DNA Microarrays The chip

4 DNA Microarrays RNA Extraction

5 DNA Microarrays Labeling the Sample Fluorescent Dye

6 DNA Microarrays Hybridization

7 DNA Microarrays Expression Measurement If the fluorescent label is attached to one spot we know that the particular complementary gene transcript was present in our cell sample. The greater the fluorescence the greater the concentration of the transcript.

8 DNA Microarrays Scanning the Microarray Measuring the intensity of the fluorescence in each spot We get a measurement of the hybridization in each spot of the microarray

9 DNA Microarrays The Data For each biological sample (individual) We get intensity measurements for thousands of genetic transcripts. The measured intensity is used as an indicator of gene expression _s_at _at _at _s_at _at _at _at _at _s_at _at _at _s_at _x_at _at _s_at _s_at _x_at _at _at _s_at _at _at _at _s_at _at

10 GEPAS/Babelomics Definitions GEPAS The Gene Expression Profile Analysis Suite is one of the most complete integrated packages of tools for microarray data analysis available over the web Babelomics Babelomics is a complete suite of web tools for functional analysis of genome scale experiments

11 GEPAS/Babelomics Pipeline

12 GEPAS Pipeline GEPAS

13 GEPAS Gene Expression Pattern Analysis Suite Montaner D., Tárraga J., Huerta-Cepas J., Burguet J., Vaquerizas J.M., Conde L., Minguez P., Vera J., Mukherjee S., Valls J., Pujana M., Alloza E., Herrero J., Al-Shahrour F., Dopazo J. Next station in microarray data analysis: GEPAS Nucl Acids Res., 2006, 34: W486-W491

14 GEPAS File format genes Tab separated file Arrays Array names #NAMES YGR138C YPR156C YOR230W YAL018C YBR287W YCL075W YDR055w YOR358W YBR006W YBR241C YCR021c YCR061W YDL024c YDR298C YER141w... col col col col col col col

15 GEPAS Gene Expression Pattern Analysis Suite

16 GEPAS Normalization

17 GEPAS Normalization Results #NAMES A01157cds_s_at A03913cds_s_at A04674cds_s_at A07543cds_s_at A09811cds_s_at A16585cds_s_at A17753cds_s_at A30543cds_s_at A44407cds_at AA108277_at AA108308_i_at AA108308_s_at AA684537_at AA684929_f_at Heart Liver Tissue

18 GEPAS Preprocessing

19 GEPAS Clustering

20 GEPAS Clustering results - ETE Viewer

21 GEPAS Differential expression

22 GEPAS Differential expression results

23 GEPAS Predictors Medina I., Montaner D., Tarraga J., Dopazo J. (2007) Prophet, a web-based tool for class prediction using microarray data Bioinformatics. 23(3):390-1

24 Babelomics Babelomics

25 Tools usage

26 WEB page

27 The Brain

28 Acknowlegdes

29 END Web page

30 Huge amount of data DNA sequencer 1474 Microbial Genomes selected: Complete - 595, Assembly - 402, Unfinished Eukaryotic Genome Sequencing Projects Selected: Complete - 24, Assembly - 164, In Progress DNA microarray: expression, genotyping, exons, tiling,...

31 Bioinformatics tools to manage the data ClustalW Blast... and more than 500 public databases and web applications