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ArrayTrack Tutorials

Tutorial Topic	Tutorial Content	Tutorial Slideshow
1. Comparing two groups (e.g., treated vs control groups). REQUIRED	Statistical methods (t-test, permutation t-test, ANOVA) for group comparison. Differentially Expressed Genes (DEGs) identification Biological interpretation (individual gene analysis) using LIB Pathway analysis (KEGG, PathArt, IPA, MetaCore, Key Molnet) Gene Ontology analysis using GOFFA	PDF 508 compliant
2. Comparing multiple groups	e.g., multiple doses, time points	PDF 508 compliant
3. VennDiagram	Determine the common genes/pathways/functions shared by two or three gene lists (extended to cross-experiment and –platform comparison and systems biology) Apply VennDiagram to the external files	PDF 508 compliant
4. Data exploring tools	Principal Component Analysis (PCA) Hierarchical Cluster Analysis (HCA) Apply HCA and PCA to the external files Extensive features in HCA	PDF 508 compliant
5. Assessing gene expression profiles using BarChart	Access BarChart from the TOOL box Access BarChart from the t-test result table Access BarChart from ChipLib and other Libs How to use BarChart for cross-experiment comparison • Assign group by color	PDF 508 compliant
6. GeneList - An important concept in ArrayTrack	Create a gene list through data filtering and statistical analysis Import/export a gene list Conduct normalization filtered by a gene lists Conduct statistical analysis (t-test/ANOVA, PCA, HCA and others) based on a gene list Export a dataset by specifying the gene list (extended for cross-platform and cross-experiment comparison)	PDF 508 compliant
7. Normalization methods	For Affymetrix platform: MAS5, RMA, DChip, Plier, Plier+16 For other platforms: 7 methods (e.g., LOWESS)	PDF 508 compliant
8. How to create your own workspace	Copy/Paste/Duplicate an experiment	PDF 508 compliant
9A Import	Manual import and batch import	PDF 508 compliant
9B Export	Options of data exporting Export a selected dataset with specifying a sub list of gene Export multiple experiments and/or platforms using selected geneID types (e.g., RefSeq)	PDF 508 compliant
10. Other useful functions	Correlation matrix IDConverter – converting one gene ID to another (e.g., from AffyID to AgilentID or GeneBank#, or LocusLinkID or vice verse) ScatterPlot – pair-wise plot JoinTable – Combine two tables SplitTable – If a table contains multiple hybridization data in column with genes in row, the function split the table into individual tables with single hybridization data. GetUniqueID – If a table contains duplicated IDs, the function pick out the unique IDs	PDF 508 compliant
11. Basic scripting for querying (raw and normalized) data and table	Query data from the database tree (How to use ) e.g., EST, EST, EST*=EST Query data in tables e.g., contain, like (%) and inlist	PDF 508 compliant
12. Using SAM through ArrayTrack	One-class, two-class, multi-class survival One-class time course, two-class time course	PDF 508 compliant
13. SimpleTox Format	For animal toxicology and toxicogenomics study, integrate microarray data with toxicological data. Data are searchable for toxicological information and microarray information. Batch import SimpleTox data including toxicological endpoints and microarray data. Contains required/optional and customized fields, not limited to non-clinical study.	PDF 508 compliant

FDA/National Center for Toxicological Research
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