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E-GEOD-20700 - Multi-level Support Vector Regression analysis to identify condition-specific regulatory networks

Status
Submitted on 9 March 2010, released on 23 March 2010, last updated on 2 May 2014
Organism
Homo sapiens
Samples (6)
Array (1)
Protocols (8)
Description
The identification of gene regulatory modules is an important yet challenging problem in computational biology. While many computational methods have been proposed to identify regulatory modules, their initial success is largely compromised by a high rate of false positives, especially when applied to human cancer studies. New strategies are needed for reliable regulatory module identification. We present a new approach, namely multi-level support vector regression (ml-SVR), to systematically identify conditionspecific regulatory modules. The approach is built upon a multi-level analysis strategy designed for suppressing false positive predictions. With this strategy, a regulatory module becomes ever more significant as more relevant gene sets are formed at finer levels. At each level, a two-stage support vector regression (SVR) method is utilized to help reduce false positive predictions by integrating binding motif information and gene expression data; a significant analysis procedure is followed to assess the significance of each regulatory module. We applied our method to breast cancer cell line data to identify condition-specific regulatory modules associated with estrogen treatment. Experimental results show that our method can identify biologically meaningful regulatory modules related to estrogen signaling and action in breast cancer. Three independent total RNA samples were extracted for each cell line (MCF-7 and MCF-7-stripped) and the samples were arrayed using Affymetrix GeneChip HG-U133A. MCF-7-stripped denotes estrogen-deprived MCF-7 human breast cancer cells, which were grown in the absence of estrogen for 96 hours. We analyzed the enriched motifs and their targets for the genes significantly down-regulated in MCF-7-stripped cells as compared to MCF-7 cells.
Experiment type
transcription profiling by array 
Contacts
Li Lily Chen <lchen06@vt.edu>, Eric P Hoffman, Jianhua Xuan, Li Chen, Rebecca B Riggins, Robert Clarke, Yue Wang
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-20700.idf.txt
Sample and data relationshipE-GEOD-20700.sdrf.txt
Raw data (1)E-GEOD-20700.raw.1.zip
Processed data (1)E-GEOD-20700.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-20700.eSet.r
Links