Case Studies (GEO Datasets) from GEO

Here we make use of the Gene Expression Omnibus (GEO) to provide example transcriptomics datasets for analysis. Each of the entries in the table below is a GEO Dataset - a curated Gene Expression study. Here are some tasks to familiarize yourself with respect to basis analyses of this type of data:

• Select a GEO Dataset
• For each GEO Dataset, you can work with the online tools provided by GEO for analysis, or your can work with the raw data provided in the links below
• If using the online tools, you will see that you can explore the clustered gene-expression profiles associated with each GEO Dataset. By clicking on the GEO Series link you can also perform differential gene expression analysis using the 'Analyze with GEO2R' button
• To work with the raw data, each of the CSV files listed in the table is a matrix (gene x sample) of gene-expression data.
• From the sample descriptions, and the experimental design described on the GEO Dataset web-page, select a group of samples to perform differential gene-expression analysis (for example this could be comparing control vs treated samples). Note that this may be a subset (or all of the samples in the file)
• For each gene, calculate a fold-change (ratio) ratio between your sample groups (e.g. treated/control) and express this as logarithm base 2
• For each gene, you could also calculate a p-value (e.g. T-test) to test whether your sample groups are statistically significantly different
• Sort the data according to the calculated ratio (and/or p-value), and identify those genes where log2 ratio > 1 or log 2 ratio < -1 or p < 0.05
• For the differential genes, use Gene Set Enrichment and/or functonal network analysis to uncover potential pathways or processes that are represented.

Study Title	GEO Link	Data
PTEN deletion mutation effect on colon cancer cells	GDS2446	mat.GDS2446.csv
Colorectal adenoma formation	GDS2947	mat.GDS2947.csv
Beta-catenin inactivation effect on intestinal crypts	GDS2984	mat.GDS2984.csv
Beta-catenin deficiency model: kidney	GDS3322	mat.GDS3322.csv
Colon carcinoma response to butyrate and aspirin	GDS332	mat.GDS332.csv
Beta-catenin depletion effect on pancreatic cancer cell line	GDS3578	mat.GDS3578.csv
Colorectal cancer tumors	GDS4382	mat.GDS4382.csv
Colorectal cancer tumors	GDS4379	mat.GDS4379.csv
Ls174T colon cancer cell line response to Wnt signaling inhibition	GDS4386	mat.GDS4386.csv
5-aza-2-deoxycytidine effect on colorectal cancer cell lines	GDS4397	mat.GDS4397.csv
Model of -catenin overexpression in embryonic kidney	GDS4449	mat.GDS4449.csv
Sporadic medulloblastomas	GDS4469	mat.GDS4469.csv
Medulloblastomas in children	GDS4471	mat.GDS4471.csv
MYC-driven medulloblastoma model	GDS4478	mat.GDS4478.csv
Colorectal cancer cell line SW480 response to Snail overexpression	GDS4596	mat.GDS4596.csv
Central nervous system primitive neuroectodermal tumors	GDS4838	mat.GDS4838.csv
Beta-catenin depletion effect on pancreatic cancer cell line	GDS5324	mat.GDS5324.csv