1. Lab # Gene Expression Data Analysis
Context
Statement of problem / Case study:
The temporal program of gene expression during a model physiological response of human cells, the response of fibroblasts to serum, was explored with a
complementary DNA microarray representing about 8600 different human genes. Genes could be clustered into groups on the basis of their temporal patterns of expression in
this program. Many features of the transcriptional program appeared to be related to the physiology of wound repair, suggesting that fibroblasts play a larger and richer role in
this complex multicellular response than had previously been appreciated.
Specification & aims Resolution process
Aim:
The purpose of this lab is to initiate a gene expression data analysis process. T1. Gene expression overview
We simulated the application on “Transcriptional Program in the Response of
Human Fibroblasts to Serum” . Now we can understand how a researcher can T1.1. Review of genomics place in OMIC- world
come to identify a significant expressed gene from microarray datasets. T1.2. Microarray data technics and process
T1.3. Data analysis cycle and tools
T2. Excel used in Genomics
Objective: use of basic excel functionalities to solve some gene
expression data analysis needs
T2.1. Column manipulation, functions used, anchor, copy with
function, sort data, search and replace
T2.2. Experiment comparison: Data pre-treatment
T1.3. Differential expressed gene from replicate experiments (SAM)
Target preparation Hybridization
Slide scanning
T3. GEPAS: Gene expression analysis pattern suite
Objective: use of the GEPAS suite to apply the whole microarray data
analyzing process on fibroblast data.
 Preprocessing
 Viewing
 Clustering
 Differential expression
Expression profile clustering
Data analysis  Classification
Acquired skills  Data mining
- Gene expression data overview
- Excel Used for genomics Conclusion: ?
- Microarray data analysis using GEPAS
16 Vishwanath R. Iyer, Science, 1999 1