Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome

doi:10.1186/1471-2148-8-2

BMC Evolutionary Biology

Volume 8

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Research article

Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome

Jason G Mezey¹^* , Sergey V Nuzhdin² , Fangfei Ye¹ and Corbin D Jones³^*

¹Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA

²Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA

³Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA

author email corresponding author email* Contributed equally

BMC Evolutionary Biology 2008, 8:2doi:10.1186/1471-2148-8-2


Published:	7 January 2008

Additional files

Additional File 1:

MA plots. Representative MA plots comparing array results within D. simulans and across species.

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Additional File 2:

Array data without mask. Processed data for the 48 Affymetrix arrays used to analyze the seven species after Loess smoothing and background correction + normalization using MAS5 without masking (see text). The list includes genes with protein coding regions from the Drosophila melanogaster genome annotation (release 4.3). Columns are as follows: A. Ensembl - the CG/CR annotation provided by Affymetrix, B. Chromosome, C. Strand - + sense/- anti-sense, D/E. Start/Stop from release 4.3, F. Affymetrix Probe Set ID, G-I. Replicates for Drosophila melanogaster, J-L. D. sechellia, M-0. D. mauritiana, P-R., D. teissieri, S-U. D. yakuba, V-Y. D. santomea, Z-BB Replicates for the 10 crosses (3 each) of D. simulans.

Format: 7Z Size: 4.6MB Download file

Additional File 3:

Array data with mask. Processed data for the 48 Affymetrix arrays used to analyze the seven species after Loess smoothing and background correction + normalization using MAS5 after probe masking (see text). A-F. Same as Additional file 2, G. Number of probes in the probe set removed by masking, H-N. Mean values for the seven species, O-BJ. see Additional file 2.

Format: 7Z Size: 3.4MB Download file

Additional File 4:

Among species sliding window analysis. p-values determined for each window in the among species analysis. The p-value is listed on the row of the first gene of the window considered. A-G. Same as Additional file 3. H. number of genes used to calculate values, I. eigenvalue statistic, J. p-value, for a window size of 2 genes, L-BL. same for window sizes 3–20.

Format: 7Z Size: 2.2MB Download file

Additional File 5:

Merged windows among species 1. Merged windows found to be significant at p-value = 0.05 in the across species analysis. A-G. Same as Additional file 3. H-Z. Window sizes 2–20.

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Additional File 6:

Merged windows among species 2. Results of repeating the sliding window analysis when removing one species at a time. Each window size presents the number of significant windows found in the analysis of all species and the numbers in parentheses reflect the range of significant windows identified when repeating the analysis removing one species at a time.

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Additional File 7:

Drosophila simulans sliding window analysis. p-values determined for each window in the D. simulans analysis. The p-value is listed on the row of the first gene of the window considered. A-BL same as Additional file 4.

Format: 7Z Size: 2.2MB Download file

Additional File 8:

Merged windows Drosophila simulans 1. Merged windows found to be significant at p-value = 0.05 in the D. simulans analysis. A-G. Same as Additional file 5. H-Z. Window sizes 2–20.

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Additional File 9:

Merged windows Drosophila simulans 2. Sets of paralogous genes and representation of these sets among significant windows identified at p-value < 0.001. A-C. Chromosome location and names of paralogous gene pairs. Note that some of these combine into larger paralog gene sets (highlighted in yellow or green). D-H. Results for the among species analysis ("AS"), i.e. window size used in the analysis, number of significant windows (numbers correspond to Table 1), number of these windows that contain paralogous, the number of paralogous in significant windows, the number of paralogs not in significant windows. I-M. Analogous results for the analysis within D. simulans ("WS").

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Additional File 10:

Over-represented gene classes. Classes of genes over-represented in co-expression clusters as identified using DAVID (see text). Results are presented for the analysis among species and for the analysis within D. simulans for window size of 2 at the p-value cutoff of p-value = 0.001. Classes with p-values < 0.05 as determined by DAVID are presented.

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