Transcriptional Profiles of Human Epithelial Cells in Response to Heat
From ArrayWiki
| PubMed ID: | 17885648 |
|---|---|
| Contact: | Jason Matthew Laramie
|
| Species: | Homo sapiens |
| Platform: | Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A |
| Number of Samples: | 13 |
| Date Range: | 11/14/2001 - 11/14/2001 |
| Experiment Quality: | 88.28 9.37 % 89.45 |
| Link to Repository: | GSE7458 |
| Original Intensity Data: | Download |
| Clean Intensity Data: | Download |
| Original PLIER Data: | Download |
| Clean PLIER Data: | Download |
| Clean CEL Files: | Download |
| Data Rank: | 
|
We hypothesized that broad-scale expression profiling would provide insight into the regulatory pathways that control gene expression in response to stress, and potentially identify novel heat-responsive genes. HEp2 cells were heated at 37 to 43 °C for 60 min to gauge the heat shock response, using as a proxy inducible HSP-70 quantified by western blot analysis. Based on these results, microarray experiments were conducted at 37, 40, 41, 42 and 43°C (3 replicates/temperature x 5 groups = 15 U95Aver2 GeneChips). Using linear modeling, we compared the sets of microarrays at 40, 41, 42 and 43°C with the 37°C baseline temperature and took the union of the genes exhibiting differential gene expression signal to create two sets of “heat shock response” genes, each set reflecting either increased or decreased RNA abundance. Leveraging human and mouse orthologous alignments, we used the two lists of co-expressed genes to predict transcription factor binding sites in silico, including those for heat shock factor 1 (HSF1) and heat shock factor 2 (HSF2) transcription factors. We discovered HSF1 and HSF2 binding sites in 15 genes not previously associated with the heat shock response. We conclude that microarray experiments coupled with upstream promoter analysis can be used to identify novel genes that respond to heat shock. Additional experiments are required to validate these putative heat shock proteins and facilitate a deeper understanding of the mechanisms involved during the stress response.
Design: Array
Type: stress response, temperature, human epithelial cells
Contents |
[edit] Contributors
- Jason M Laramie
- Philip Chung
- Buddy Brownstein
- Gary D Stormo
- Perren Cobb
[edit] Protocols
[edit] References
[edit] Links
GEO Accession for this experiment: GSE7458. (Public on Apr 10 2007)
PubMed abstract: 17885648
RAW data: tar file.
[edit] Analysis
 Before Normalization |
 After Normalization & Cleaning |
[edit] Samples/Quality Control
| Sample | Date Scanned | Source Link | Probe Variance Data | Artifact Mask | Quality Score |
|---|---|---|---|---|---|
| Hep2_43_rep3 | 11/14/01 18:49:21 | GSM180458 | 
| 
| 95.4211 1.64 % 96.89 |
| Hep2_37_rep1 | 11/14/01 17:16:46 | GSM180460 | 
| 
| 95.5784 0.52 % 97.53 |
| Hep2_37_rep2 | 11/14/01 15:59:17 | GSM180463 | 
| 
| 95.5736 10.05 % 92.76 |
| Hep2_37_rep3 | 11/14/01 17:05:35 | GSM180464 | 
| 
| 95.6899 0.52 % 97.58 |
| Hep2_40_rep1 | 11/14/01 16:09:52 | GSM180465 | 
| 
| 96.3351 0.89 % 97.72 |
| Hep2_40_rep2 | 11/14/01 16:54:21 | GSM180468 | 
| 
| 91.7654 26.13 % 82.82 |
| Hep2_41_rep1 | 11/14/01 16:20:18 | GSM180474 | 
| 
| 96.4175 0.76 % 97.83 |
| Hep2_41_rep2 | 11/14/01 16:31:48 | GSM180477 | 
| 
| 95.8656 0.48 % 97.69 |
| Hep2_41_rep3 | 11/14/01 17:47:13 | GSM180483 | 
| 
| 93.9617 65.39 % 64.28 |
| Hep2_42_rep2 | 11/14/01 18:07:48 | GSM180494 | 
| 
| 95.4463 1.24 % 97.1 |
| Hep2_42_rep3 | 11/14/01 18:28:41 | GSM180501 | 
| 
| 95.4381 0.25 % 97.6 |
| Hep2_43_rep1 | 11/14/01 18:17:58 | GSM180512 | 
| 
| 96.1991 1.02 % 97.59 |
| Hep2_43_rep2 | 11/14/01 18:38:55 | GSM180520 | 
| 
| 92.2191 22.36 % 84.93 |
