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Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation
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| Zeitschriftentitel: | Bioinformatics |
|---|---|
| Personen und Körperschaften: | , , |
| In: | Bioinformatics, 23, 2007, 11, S. 1356-1362 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Oxford University Press (OUP)
|
| Schlagwörter: |
| author_facet |
Kemp, Daniel M. Nirmala, N. R. Szustakowski, Joseph D. Kemp, Daniel M. Nirmala, N. R. Szustakowski, Joseph D. |
|---|---|
| author |
Kemp, Daniel M. Nirmala, N. R. Szustakowski, Joseph D. |
| spellingShingle |
Kemp, Daniel M. Nirmala, N. R. Szustakowski, Joseph D. Bioinformatics Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| author_sort |
kemp, daniel m. |
| spelling |
Kemp, Daniel M. Nirmala, N. R. Szustakowski, Joseph D. 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btm116 <jats:title>Abstract</jats:title><jats:p>Motivation: We describe an extension of the pathway-based enrichment approach for analyzing microarray data via a robust test for transcriptional variance. The use of a variance test is intended to identify additional patterns of transcriptional regulation in which many genes in a pathway are up- and down-regulated. Such patterns may be indicative of the reciprocal regulation of pathway activators and inhibitors or of the differential regulation of separate biological sub-processes and should extend the number of detectable patterns of transcriptional modulation.</jats:p><jats:p>Results: We validated this new statistical approach on a microarray experiment that captures the temporal transcriptional profile of muscle differentiation in mouse C2C12 cells. Comparisons of the transcriptional state of myoblasts and differentiated myotubes via a robust variance test implicated several novel pathways in muscle cell differentiation previously overlooked by a standard enrichment analysis. Specifically, pathways involved in cell structure, calcium-mediated signaling and muscle-specific signaling were identified as differentially modulated based on their increased transcriptional variance. These biologically relevant results validate this approach and demonstrate the flexible nature of pathway-based methods of data analysis.</jats:p><jats:p>Availability: The software is available as Supplementary Material.</jats:p><jats:p>Contact: joseph.szustakowski@novartis.com</jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation Bioinformatics |
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| title |
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_unstemmed |
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_full |
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_fullStr |
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_full_unstemmed |
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_short |
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_sort |
extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| topic |
Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| url |
http://dx.doi.org/10.1093/bioinformatics/btm116 |
| publishDate |
2007 |
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1356-1362 |
| description |
<jats:title>Abstract</jats:title><jats:p>Motivation: We describe an extension of the pathway-based enrichment approach for analyzing microarray data via a robust test for transcriptional variance. The use of a variance test is intended to identify additional patterns of transcriptional regulation in which many genes in a pathway are up- and down-regulated. Such patterns may be indicative of the reciprocal regulation of pathway activators and inhibitors or of the differential regulation of separate biological sub-processes and should extend the number of detectable patterns of transcriptional modulation.</jats:p><jats:p>Results: We validated this new statistical approach on a microarray experiment that captures the temporal transcriptional profile of muscle differentiation in mouse C2C12 cells. Comparisons of the transcriptional state of myoblasts and differentiated myotubes via a robust variance test implicated several novel pathways in muscle cell differentiation previously overlooked by a standard enrichment analysis. Specifically, pathways involved in cell structure, calcium-mediated signaling and muscle-specific signaling were identified as differentially modulated based on their increased transcriptional variance. These biologically relevant results validate this approach and demonstrate the flexible nature of pathway-based methods of data analysis.</jats:p><jats:p>Availability: The software is available as Supplementary Material.</jats:p><jats:p>Contact: joseph.szustakowski@novartis.com</jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> |
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| author | Kemp, Daniel M., Nirmala, N. R., Szustakowski, Joseph D. |
| author_facet | Kemp, Daniel M., Nirmala, N. R., Szustakowski, Joseph D., Kemp, Daniel M., Nirmala, N. R., Szustakowski, Joseph D. |
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| description | <jats:title>Abstract</jats:title><jats:p>Motivation: We describe an extension of the pathway-based enrichment approach for analyzing microarray data via a robust test for transcriptional variance. The use of a variance test is intended to identify additional patterns of transcriptional regulation in which many genes in a pathway are up- and down-regulated. Such patterns may be indicative of the reciprocal regulation of pathway activators and inhibitors or of the differential regulation of separate biological sub-processes and should extend the number of detectable patterns of transcriptional modulation.</jats:p><jats:p>Results: We validated this new statistical approach on a microarray experiment that captures the temporal transcriptional profile of muscle differentiation in mouse C2C12 cells. Comparisons of the transcriptional state of myoblasts and differentiated myotubes via a robust variance test implicated several novel pathways in muscle cell differentiation previously overlooked by a standard enrichment analysis. Specifically, pathways involved in cell structure, calcium-mediated signaling and muscle-specific signaling were identified as differentially modulated based on their increased transcriptional variance. These biologically relevant results validate this approach and demonstrate the flexible nature of pathway-based methods of data analysis.</jats:p><jats:p>Availability: The software is available as Supplementary Material.</jats:p><jats:p>Contact: joseph.szustakowski@novartis.com</jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> |
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| spelling | Kemp, Daniel M. Nirmala, N. R. Szustakowski, Joseph D. 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btm116 <jats:title>Abstract</jats:title><jats:p>Motivation: We describe an extension of the pathway-based enrichment approach for analyzing microarray data via a robust test for transcriptional variance. The use of a variance test is intended to identify additional patterns of transcriptional regulation in which many genes in a pathway are up- and down-regulated. Such patterns may be indicative of the reciprocal regulation of pathway activators and inhibitors or of the differential regulation of separate biological sub-processes and should extend the number of detectable patterns of transcriptional modulation.</jats:p><jats:p>Results: We validated this new statistical approach on a microarray experiment that captures the temporal transcriptional profile of muscle differentiation in mouse C2C12 cells. Comparisons of the transcriptional state of myoblasts and differentiated myotubes via a robust variance test implicated several novel pathways in muscle cell differentiation previously overlooked by a standard enrichment analysis. Specifically, pathways involved in cell structure, calcium-mediated signaling and muscle-specific signaling were identified as differentially modulated based on their increased transcriptional variance. These biologically relevant results validate this approach and demonstrate the flexible nature of pathway-based methods of data analysis.</jats:p><jats:p>Availability: The software is available as Supplementary Material.</jats:p><jats:p>Contact: joseph.szustakowski@novartis.com</jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation Bioinformatics |
| spellingShingle | Kemp, Daniel M., Nirmala, N. R., Szustakowski, Joseph D., Bioinformatics, Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| title | Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_full | Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_fullStr | Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_full_unstemmed | Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_short | Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_sort | extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| title_unstemmed | Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation |
| topic | Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| url | http://dx.doi.org/10.1093/bioinformatics/btm116 |