Selecting Relevant Genes with a Spectral Approach
Array technologies have made it possible to record simultaneously the expression pattern of thousands of genes. A fundamental problem in the analysis of gene expression data is the identification of highly relevant genes that either discriminate between phenotypic labels or are important with respec...
| Main Authors: | , , |
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| Language: | en_US |
| Published: |
2004
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| Online Access: | http://hdl.handle.net/1721.1/7282 |
| _version_ | 1826197608582873088 |
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| author | Wolf, Lior Amnon Shashua, Mukherjee, Sayan |
| author_facet | Wolf, Lior Amnon Shashua, Mukherjee, Sayan |
| author_sort | Wolf, Lior |
| collection | MIT |
| description | Array technologies have made it possible to record simultaneously the expression pattern of thousands of genes. A fundamental problem in the analysis of gene expression data is the identification of highly relevant genes that either discriminate between phenotypic labels or are important with respect to the cellular process studied in the experiment: for example cell cycle or heat shock in yeast experiments, chemical or genetic perturbations of mammalian cell lines, and genes involved in class discovery for human tumors. In this paper we focus on the task of unsupervised gene selection. The problem of selecting a small subset of genes is particularly challenging as the datasets involved are typically characterized by a very small sample size ?? the order of few tens of tissue samples ??d by a very large feature space as the number of genes tend to be in the high thousands. We propose a model independent approach which scores candidate gene selections using spectral properties of the candidate affinity matrix. The algorithm is very straightforward to implement yet contains a number of remarkable properties which guarantee consistent sparse selections. To illustrate the value of our approach we applied our algorithm on five different datasets. The first consists of time course data from four well studied Hematopoietic cell lines (HL-60, Jurkat, NB4, and U937). The other four datasets include three well studied treatment outcomes (large cell lymphoma, childhood medulloblastomas, breast tumors) and one unpublished dataset (lymph status). We compared our approach both with other unsupervised methods (SOM,PCA,GS) and with supervised methods (SNR,RMB,RFE). The results clearly show that our approach considerably outperforms all the other unsupervised approaches in our study, is competitive with supervised methods and in some case even outperforms supervised approaches. |
| first_indexed | 2024-09-23T10:50:15Z |
| id | mit-1721.1/7282 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:50:15Z |
| publishDate | 2004 |
| record_format | dspace |
| spelling | mit-1721.1/72822019-04-15T00:40:28Z Selecting Relevant Genes with a Spectral Approach Wolf, Lior Amnon Shashua, Mukherjee, Sayan AI Array technologies have made it possible to record simultaneously the expression pattern of thousands of genes. A fundamental problem in the analysis of gene expression data is the identification of highly relevant genes that either discriminate between phenotypic labels or are important with respect to the cellular process studied in the experiment: for example cell cycle or heat shock in yeast experiments, chemical or genetic perturbations of mammalian cell lines, and genes involved in class discovery for human tumors. In this paper we focus on the task of unsupervised gene selection. The problem of selecting a small subset of genes is particularly challenging as the datasets involved are typically characterized by a very small sample size ?? the order of few tens of tissue samples ??d by a very large feature space as the number of genes tend to be in the high thousands. We propose a model independent approach which scores candidate gene selections using spectral properties of the candidate affinity matrix. The algorithm is very straightforward to implement yet contains a number of remarkable properties which guarantee consistent sparse selections. To illustrate the value of our approach we applied our algorithm on five different datasets. The first consists of time course data from four well studied Hematopoietic cell lines (HL-60, Jurkat, NB4, and U937). The other four datasets include three well studied treatment outcomes (large cell lymphoma, childhood medulloblastomas, breast tumors) and one unpublished dataset (lymph status). We compared our approach both with other unsupervised methods (SOM,PCA,GS) and with supervised methods (SNR,RMB,RFE). The results clearly show that our approach considerably outperforms all the other unsupervised approaches in our study, is competitive with supervised methods and in some case even outperforms supervised approaches. 2004-10-20T21:05:21Z 2004-10-20T21:05:21Z 2004-01-27 AIM-2004-002 CBCL-234 http://hdl.handle.net/1721.1/7282 en_US AIM-2004-002 CBCL-234 2062939 bytes 836436 bytes application/postscript application/pdf application/postscript application/pdf |
| spellingShingle | AI Wolf, Lior Amnon Shashua, Mukherjee, Sayan Selecting Relevant Genes with a Spectral Approach |
| title | Selecting Relevant Genes with a Spectral Approach |
| title_full | Selecting Relevant Genes with a Spectral Approach |
| title_fullStr | Selecting Relevant Genes with a Spectral Approach |
| title_full_unstemmed | Selecting Relevant Genes with a Spectral Approach |
| title_short | Selecting Relevant Genes with a Spectral Approach |
| title_sort | selecting relevant genes with a spectral approach |
| topic | AI |
| url | http://hdl.handle.net/1721.1/7282 |
| work_keys_str_mv | AT wolflior selectingrelevantgeneswithaspectralapproach AT amnonshashua selectingrelevantgeneswithaspectralapproach AT mukherjeesayan selectingrelevantgeneswithaspectralapproach |