Gene regulatory networks in lactation: identification of global principles using bioinformatics

Additional file 1:

Additional data file 1 is an Excel spreadsheet that lists genes with a standard correlation of 0.90 or better with the first principal component.

Format: XLS Size: 403KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

Additional data file 2 is an Excel spreadsheet that lists genes that are suppressed during lactation. These genes are down-regulated by L2 relative to P17 and up-regulated by I2 relative to L9.

Format: XLS Size: 429KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 5:

Additional data file 5 is an Excel file that lists genes that are members of the Involution Gene Set. These genes are differentially regulated between time points L9 and I2. Two spreadsheets are provided in the file, one for up-regulated and one for down-regulated genes.

Format: XLS Size: 1MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 7:

Additional data file 7 is an Excel file of genes that are associated with the GO terms in Table 2 and are members of the Pregnancy Gene Set (i.e. differentially regulated between time points P1 and P19). Two spreadsheets are provided in the file, one for up-regulated and one for down-regulated genes.

Format: XLS Size: 111KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 8:

Additional data file 8 is an Excel file of genes that are associated with the GO terms in Table 3 and are members of the Lactation Gene Set (i.e. differentially regulated between time points P19 and L9). Two spreadsheets are provided in the file, one for up-regulated and one for down-regulated genes.

Format: XLS Size: 335KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 9:

Additional data file 9 is an Excel file of genes that are associated with the GO terms in Table 4 and are members of the Involution Gene Set (i.e. differentially regulated between time points L9 and I2). Two spreadsheets are provided in the file, one for up-regulated and one for down-regulated genes.

Format: XLS Size: 212KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

Additional data file 3 is an Excel file that lists genes that are members of the Pregnancy Gene Set. These genes are differentially regulated between time points P1 and P19. Two spreadsheets are provided in the file, one for up-regulated and one for down-regulated genes.

Format: XLS Size: 1.8MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 4:

Additional data file 4 is an Excel file that lists genes that are members of the Lactation Gene Set. These genes are differentially regulated between time points P19 and L9. Two spreadsheets are provided in the file, one for up-regulated and one for down-regulated genes.

Format: XLS Size: 794KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 19:

Additional data file 19 is an Excel file that provides the adjusted and unadjusted p-values and associated genes for all pathways which contain one or more differentially regulated genes. The file contains three spreadsheets, one each for the Pregnancy, Lactation, and Involution Gene Sets.

Format: XLS Size: 97KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 20:

Additional data file 20 is a Word document that contains pathway diagrams for the significant pathways associated with the Pregnancy Gene Set.

Format: DOC Size: 4.3MB Download file

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Additional file 21:

Additional data file 21 is a Word document that contains pathway diagrams for the significant pathways associated with the Lactation Gene Set.

Format: DOC Size: 4.5MB Download file

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Additional file 22:

Additional data file 22 is a Word document that contains pathway diagrams for the significant pathways associated with the Involution Gene Set.

Format: DOC Size: 7.7MB Download file

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Additional file 10:

Additional data file 10 is an Excel file that provides HGNC symbols, Swissprot identifiers, and descriptions for each protein interaction pair associated with Figure 8. Six spreadsheets are provided in the file, one for each of the networks in Figure 8.

Format: XLS Size: 3.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 11:

Additional data file 11, an SWF movie file, is a 3D animation of the network in Figure 8A (the within-set pregnancy network) in which the nodes are labeled with HGNC symbols. The HGNC symbols, Swissprot identifiers, and descriptions for each protein interaction pair are given in Additional file 10.

Format: SWF Size: 4.8MB Download file

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Additional file 12:

Additional data file 12, an SWF movie file, is a 3D animation of the trivial network in Figure 8B (the within-set lactation network) in which the nodes are labeled with HGNC symbols. The HGNC symbols, Swissprot identifiers, and descriptions for each protein interaction pair are given in Additional file 10.

Format: SWF Size: 37KB Download file

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Additional file 13:

Additional data file 13, an SWF movie file, is a 3D animation of the network in Figure 8C (the within-set involution network) in which the nodes are labeled with HGNC symbols. The HGNC symbols, Swissprot identifiers, and descriptions for each protein interaction pair are given in Additional file 10.

Format: SWF Size: 7.9MB Download file

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Additional file 14:

Additional data file 14, an SWF movie file, is a 3D animation of the network in Figure 8D (the pregnancy network) in which the nodes are labeled with HGNC symbols. The HGNC symbols, Swissprot identifiers, and descriptions for each protein interaction pair are given in Additional file 10.

Format: SWF Size: 8.4MB Download file

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Additional file 15:

Additional data file 15, an SWF movie file, is a 3D animation of the network in Figure 8E (the lactation network) in which the nodes are labeled with HGNC symbols. The HGNC symbols, Swissprot identifiers, and descriptions for each protein interaction pair are given in Additional file 10.

Format: SWF Size: 9.5MB Download file

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Additional file 16:

Additional data file 16, an SWF movie file, is a 3D animation of the network in Figure 8F (the involution network) in which the nodes are labeled with HGNC symbols. The HGNC symbols, Swissprot identifiers, and descriptions for each protein interaction pair are given in Additional file 10.

Format: SWF Size: 1.9MB Download file

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Additional file 17:

Additional data file 17 is an Excel file that provides HGNC symbols, Swissprot identifiers, and descriptions for each protein interaction pair that comprises the comprehensive lactation network in Figure 9.

Format: XLS Size: 240KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 18:

Additional data file 18, an SWF movie file, is a 3D animation of the network in Figure 9 (comprehensive lactation network) in which the nodes are labeled with HGNC symbols. The HGNC symbols, Swissprot identifiers, and descriptions for each protein interaction pair are given in Additional file 17.

Format: SWF Size: 5.9MB Download file

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Additional file 23:

Additional data file 23 is a Word document that contains manually curated general and mammary-specific functions of the major hubs of the comprehensive lactation network in Figure 9.

Format: DOC Size: 184KB Download file

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Additional file 6:

Additional data file 6 is an Excel file that lists genes that are members of the Literature Gene Set. These genes have been co-published with the keyword 'lactation'.

Format: XLS Size: 166KB Download file

This file can be viewed with: Microsoft Excel Viewer