Genome Biology
Volume 9
Issue 7

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Naxerova K
Bult CJ
Peaston A
Fancher K
Knowles BB
Kasif S
Kohane IS

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Naxerova K
Bult CJ
Peaston A
Fancher K
Knowles BB
Kasif S
Kohane IS
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Research

Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers

Kamila Naxerova¹ , Carol J Bult² , Anne Peaston² , Karen Fancher² , Barbara B Knowles² , Simon Kasif¹^,3 and Isaac S Kohane¹

¹Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology, Longwood Avenue, Boston, MA 02115, USA

²The Jackson Laboratory, Main Street, Bar Harbor, ME 04609, USA

³Department of Biomedical Engineering, Boston University, Cummington Street, Boston, MA 02215, USA

author email corresponding author email

Genome Biology 2008, 9:R108doi:10.1186/gb-2008-9-7-r108


Published:	8 July 2008

Subject areas: Cancer, Development, Genome studies

Additional files

Additional data file 1:

Frequency plots for all cancer types and all developmental time series.

Format: PDF Size: 641KB Download file

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Additional data file 2:

Frequency plots for all cancers and all time series after CC subtraction.

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Additional data file 3:

Frequency plots for the top 450 differentially expressed genes in CRCC1 and CRCC2.

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Additional data file 4:

Heatmap of probability distribution slopes after CC subtraction (analogously to Figure 3).

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Additional data file 5:

Heatmap of enrichment p-values for gene sets that ranked among the 20 most enriched in the downregulated genes of either group 1, 2 or 3.

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Additional data file 6:

Detailed annotation for all data sets used in this study.

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Additional data file 7:

Raw data for the lung development validation time series (after RMA-normalization).

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Additional data file 8:

This shows a bimodal distribution with the left peak containing group 3 tumors, the right peak containing group 1 tumors and intermediate cases (group 2) falling in between.

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Additional data file 9:

Probability distribution plots and linear regression fits for all cancers and all time series.

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Additional data file 10:

The same data as additional data file 9, but after CC subtraction.

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