* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Loading experiment results - Exploratory Gene Association Networks
Survey
Document related concepts
Transcript
EGAN tutorial: Loading experiment results October, 2009 Jesse Paquette UCSF Helen Diller Family Comprehensive Cancer Center [email protected] Preamble • This document has many slides with multi-step animations – Best viewed in Slide Show mode • The EGAN graphical user interface is evolving – Icons may change – Menus may change – Button/widget placement may change – This document probably won’t change as quickly – Please contact the developers if you notice major discrepancies between this and EGAN Loading experiment results: An overview • EGAN is designed to help you interpret the results of exploratory assays • EGAN does not actually do the multivariate statistical analysis for your experiment – It picks up where many useful analysis programs stop: at the gene list • If the entities measured in an assay can be mapped to genes, the results can be loaded in EGAN – – – – Expression microarrays MS/MS peptide identifications Genome-wide SNP/CNV assays Next-gen sequencing – DNA methylation assays – ChIP chips Loading experiment results: An overview • EGAN works best when you load results for all entities measured in the assay – i.e., don’t apply a p-value cutoff on the results before loading into EGAN – Just because a gene missed the cutoff at p < 0.001, there’s still a good chance that it is a significant hit • Especially if it is related to other top hit genes – EGAN will allow you to adjust the statistic/p-value cutoff dynamically • Then you can directly observe how networks/enrichment scores change with different cutoff values – Of course you can still load post-cutoff experiment results • If that’s all you have… Loading experiment results into EGAN Loading experiment results into EGAN: The file format • Tab-delimited text – Easy to create in Excel from existing result files • Header line required – Header of statistic (second) column will become the experiment name in EGAN • Three columns – 1) Entity ID • i.e. probe set ID, UniProt ID, refSNP ID, etc. • You can use any IDs that can be mapped to Entrez Gene IDs • EGAN provides a wide variety of mapping file options – HUGO Gene Symbol, AffymetrixAgilent/Illumina IDs, GenBank, Ensembl, UniProt, etc. • EGAN expects that all entity IDs are the same type – 2) Statistic (fold-change, regression coefficient, log-odds ratio, etc.) • EGAN visualization schemes are best when the statistic column is centered around 0 • Ratio and fold-change data can be 0-centered by logarithm – 3) P-value (unadjusted, adjusted or q-value) Loading experiment results into EGAN: An example Header line: the statistic (second) column header should be descriptive Each row represents the analysis result for one entity in the experiment Three columns: ID, statistic, p-value Loading experiment results into EGAN: An example Save as tab-delimited text Loading experiment results into EGAN: An example • Download or construct an experiment result file – This example will use two pre-made experiment result files (download these files to follow along) • Affymetrix (expression) predictors of Herceptin resistance in HER2 over-expressing breast cancer cell lines • aCGH (copy number) predictors of Herceptin resistance in HER2 over-expressing breast cancer cell lines – …and one custom mapping file • Launch EGAN H. sapiens Loading experiment results into EGAN: An example Click “Browse…” Click “Browse…” This experiment result Enrichment calculations in EGAN are dependent on file uses Affymetrix how we define the background population of genes. HG-U133A probe set In this case we only want genes to be in the identifiers. background if they are present in all experiment For simplicity’s sake, results. Select “Affymetrix HGwe’re not going toresults cover Select Selectyour the experiment aCGH experiment and click Now both experiment Select the mapping file and For the aCGH clones we We “Specify want load a new experiment U133A” from the items 3-5 right now. and to click empirical “Specify data empirical set” The expression results are ready Select “intersection” from the drop-down are ready to list. be loaded. click “Specify mapping file” mapping have a custom drop-down menu. data set” to be loaded. Let’s load the file.Click “Add Experiment”. aCGH results. There’s thing to Clickone “Addmore Experiment” consider before launching Click on “6) Experiments” Click “Browse…” ClickEGAN...click “New Data Set”. on “5) Gene Nodes”. Finally, click “Finish – Launch EGAN” Loading experiment results into EGAN: An example Whenever you change the network configuration by adding or removing files, you will be given the option to save the new configuration to a tab-delimited text file. If you choose to save a .config file, next time you will only need to specify that file (item 3 in the Launch EGAN Wizard). Loading experiment results into EGAN: An example Your experiments are now accessible in EGAN: as columns in the Entrez Gene Node Table and as rows in the Experiments Table. Questions/comments? • Visit http://groups.google.com/group/ucsf-egan for downloads, documentation and discussion – Requires an account with Google Groups