Schedule 1 2 3 4 Biological Functional Databases

: : : Schedule. 1. 2. 3. 4. Biological (Functional) Databases Threshold-based and threshold free methods Threshold-based example: Fati. GO. Threshold free example 1: Fatis. Scan.

Two-steps approach reproduces pre-genomics paradigms experiments pass test test test . . annotation no annotation : : Context and cooperation between genes is ignored

A previous step of gene selection causes loss of information and makes the test insensitive Significantly over-expressed in B p<0. 05 statistic t-test with two tails. - AB GO 1 GO 2 Very few genes selected to arrive to a significant conclussion on GO 1 and GO 2 If a threshold based on the experimental values is applied, and the resulting selection of genes compared for enrichment of a functional term, this might not be found Functional Classes expressed as blocks in A and B Significantly over-expressed in A +

Threshold-free approach Including information in the procedure of gene selection Functional label A List of genes + A B C Functional label B Blocks of genes with significant functional term A annotated • Genes are ranked by any biological criteria (expression value, positive selection, etc). Homogeneously distributed Functional term C • Fati. Scan searchs for the distribution of the blocks of functionally related genes across the list. Functional label C • To detect significant terms a segmentation test is performed. - Blocks of genes with significant functional term B annotated • Properties of groups of genes are considered.

Gene Set Enrichment Just ONE list (ranked)

: : : Exercise 3: Fati. Scan Selected data Mootha et al. Nat Genet 2003

-Run. T-rex for differential expression analysis. Files: fatiscan_diabetes_mootha_array. txt fatiscan_diabetes_mootha_classes. txt Results T-Rex Run T-Rex here http: //www. gepas. org/

-Examine Results and send to Fati. Scan- Send to Fati. Scan here Check the FDR adjusted p-value

-Run Fatiscan with statistic-ranked list In Fati. Scan input form: select the organism Homo sapiens, Gene Ontology: biological process with the default filtering, 30 partitions, Two tailed Fisher's exact test, and press Run. As the sorted list comes from GEPAS it will automatically detect the sorting and the labels.

Significantly altered KEGG Pathways (MGT y DM 2/IGT):