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| Status |
Public on Sep 15, 2008 |
| Title |
Gene-level summary data from Affymetrix Human Exon 1.0 ST array |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
The Affymetrix Human Exon 1.0 ST array was used to measure differential splicing patterns in archived RNA isolated from 26 of 80 children (11 Rejectors and 15 Non-Rejectors). The gene-level probe summaries reported in this series were computed using the Affymetrix Power Tools (APT) software and 'rma-sketch' normalization method.
Keywords: Affymetrix 1.0 ST exon array; gene-level analysis
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| Overall design |
The gene-level normalized intensities (NI) were computed with the MiDAS algorithm and both the splicing index (SI) and Student's t-test p-values (two-sided) were computed on the NI values in R. To remove low expressed gene-level probes, those with values less than 3.5 (log2 scale) in >50% of the samples in either group were filtered out leaving 17,242 of the original 22,011 probes. Those gene-level probes that were highly differentially expressed between groups were also removed using a fold change threshold of log2. This step accounts for the tendency for the genelevel probe set intensities in each group to be "disproportionately affected by background noise or saturation" (Affymetrix Technical notes).
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| Contributor(s) |
Sindhi R, Higgs BW |
| Citation(s) |
18639552 |
| Submission date |
May 06, 2008 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Rakesh Sindhi |
| Organization name |
Children’s Hospital of Pittsburgh
|
| Department |
Hillman Center for Pediatric Transplantation
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| Street address |
3705 Fifth Avenue
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
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| Platforms (1) |
| GPL5175 |
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version] |
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| Samples (26)
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| This SubSeries is part of SuperSeries: |
| GSE11361 |
Genetic variants in Major Histocompatibility Complex-linked genes Associate with Pediatric Liver Transplant Rejection |
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| Relations |
| BioProject |
PRJNA109213 |
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