Gene Expression Lab Summary
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Gene Expression Lab Summary

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Gene Expression Lab Summary Gene Expression Lab Summary Presentation Transcript

  • 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 processAim:The purpose of this lab is to initiate a gene expression data analysis process. T1. Gene expression overviewWe simulated the application on “Transcriptional Program in the Response ofHuman Fibroblasts to Serum” . Now we can understand how a researcher can T1.1. Review of genomics place in OMIC- worldcome 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