Data from: Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback

Morris MRJ, Richard R, Leder EH, Barrett RDH, Aubin-Horth N, Rogers SM

Date Published: June 3, 2014

DOI: http://dx.doi.org/10.5061/dryad.5q65k

 

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Title MATLAB Statistics for Gene Expression Data
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Description This file contains the results of the full model and the individual contrasts, for each of 14 208 genes. The first six worksheets provide data from the full model: p-values for each gene for origin, temperature, population(origin), and the interaction term, q-values for the same, SSQ and degrees of freedom for the same, coefficients for each origin, temperature, population(origin), and interaction, and a summary of the significantly expressed genes for origin alone, temperature alone, both origin and temperature, and the interaction term, under p-value of 0.05 and q-values of 0.05 and 0.1.The remaining three worksheets contain a summary of the number of genes differentially expressed by temperature under the independent contrasts, including the total number, freshwater total, marine total, both marine and freshwater, only freshwater, and only marine, for p-value of 0.05 and q-values of 0.05 and 0.1. p-values and q-values for freshwater and marine contrasts follow.
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Title Code used for MATLAB
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Description This file contains the code used to generate the data for the marine and freshwater stickleback contrasts.
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Title Normalized and Filtered Gene Expression Data
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Description This file contains the LIMMA output for normalized and filtered microarray data. This data was then used in MATLAB. Each column contains a new microarray. Rows 1-7 provide descriptive data for each microarray, including population (Hoggan Lake freshwater, HLF; Cranby Lake freshwater, CLF; Oyster Lagoon marines, OLM; Little Campbell River marines, LCM), temperature (7 or 22 degrees C), Origin (marine, freshwater), the tank number the fish was raised in, sex of the fish, the microarray slide the microarray was on, and the microarray filename.
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Title LIMMA Supplemental Results
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Description LIMMA output file using all 20 021 genes present on the microarray, as described in the supplemental information. Within-population contrasts were performed. Coefficients for all four populations, and associated t-statistics and p-values, along with F-statistics and p-values, are provided. Columns T,U,V,W: 0 = not significantly influenced by temperature; 1 = up-regulated at 22 degrees C; -1 = up-regulated at 7 degrees C. The microarray probe name and its associated Ensembl transcript ID follow.
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Title LIMMA Targets File
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Description This text file contains information pertaining to each microarray (sex, population, temperature, tank, array number, array file name) used by LIMMA to Normalize the data for Matlab, or to provide supplemental results.
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Title Transcript ID
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Description This file contains a key for matching "Custxxx" microarray probenames with their respective Ensembl transcript ID.
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Title Feature Extraction Output for Microarray Slide No. 3
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Description This file contains the extracted data from all eight microarrays present on microarray slide number 3. For information on the output, see the Agilent Feature Extraction guide cited in text.
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Title Feature Extraction Output for Microarray Slide No. 6
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Description This file contains the extracted data from the seven microarrays present on microarray slide number 6 that passed quality control. For information on the output, see the Agilent Feature Extraction guide cited in text.
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Title Feature Extraction Output for Microarray Slide No. 7
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Description This file contains the extracted data from all eight microarrays present on microarray slide number 7. For information on the output, see the Agilent Feature Extraction guide cited in text.
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Title Feature Extraction Output for Microarray Slide No. 8
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Description This file contains the extracted data from all four microarrays present on microarray slide number 8. For information on the output, see the Agilent Feature Extraction guide cited in text.
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Title Feature Extraction Output for Microarray Slide No. 9
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Description This file contains the extracted data from all seven microarrays present on microarray slide number 9 that passed quality control. For information on the output, see the Agilent Feature Extraction guide cited in text.
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Title Feature Extraction Output for Microarray Slide No. 10
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Description This file contains the extracted data from all eight microarrays present on microarray slide number 10. For information on the output, see the Agilent Feature Extraction guide cited in text.
Download MicroarrayNo10.xlsx (84.84 Mb)
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Title Summary of Significantly Enriched Gene Classes
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Description This file contains the full list of enriched gene classes, and the members of each gene class. There are five worksheets: enriched gene classes in marine stickleback at 22 degrees C, enriched gene classes in marine stickleback at 7 degrees C, enriched gene classes in freshwater stickleback at 22 degrees C, enriched gene classes in freshwater stickleback at 7 degrees C, and a key that identifies probe number with Ensembl transcript ID.
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Title Hierarchical GO Graph, Marine 22 deg C, Biological Processes
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Description Significantly enriched gene classes shown in hierarchical graph, for biological processes.
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Title Hierarchical GO Graph, Marine 22 deg C, Molecular Processes
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Description Significantly enriched gene classes shown in hierarchical graph, for molecular processes.
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Title Hierarchical GO Graph, Marine 22 deg C, Cellular Processes
Downloaded 37 times
Description Significantly enriched gene classes shown in hierarchical graph, for cellular processes.
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Title Hierarchical GO Graph, Marine 7 deg C, Molecular Processes
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Description Significantly enriched gene classes shown in hierarchical graph, for molecular processes.
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Title Hierarchical GO Graph, Marine 7 deg C, Biological Processes
Downloaded 40 times
Description Significantly enriched gene classes shown in hierarchical graph, for biological processes.
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Title Hierarchical GO Graph, Marine 7 deg C, Cellular Processes
Downloaded 31 times
Description Significantly enriched gene classes shown in hierarchical graph, for cellular processes.
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Title Hierarchical GO Graph, Freshwater 22 deg C, Biological Processes
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Description Significantly enriched gene classes shown in hierarchical graph, for biological processes.
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Title Hierarchical GO Graph, Freshwater 22 deg C, Cellular Processes
Downloaded 42 times
Description Significantly enriched gene classes shown in hierarchical graph, for cellular processes.
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Title Hierarchical GO Graph, Freshwater 22 deg C, Molecular Processes
Downloaded 40 times
Description Significantly enriched gene classes shown in hierarchical graph, for molecular processes.
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Title Hierarchical GO Graph, Freshwater 7 deg C, Biological Processes
Downloaded 49 times
Description Significantly enriched gene classes shown in hierarchical graph, for biological processes.
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Title Hierarchical GO Graph, Freshwater 7 deg C, Cellular Processes
Downloaded 33 times
Description Significantly enriched gene classes shown in hierarchical graph, for cellular processes.
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Title Hierarchical GO Graph, Freshwater 7 deg C, Molecular Processes
Downloaded 47 times
Description Significantly enriched gene classes shown in hierarchical graph, for molecular processes.
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When using this data, please cite the original publication:

Morris MRJ, Richard R, Leder EH, Barrett RDH, Aubin-Horth N, Rogers SM (2014) Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback. Molecular Ecology 23(13): 3226–3240. http://dx.doi.org/10.1111/mec.12820

Additionally, please cite the Dryad data package:

Morris MRJ, Richard R, Leder EH, Barrett RDH, Aubin-Horth N, Rogers SM (2014) Data from: Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.5q65k
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