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Spatial expression of transcription factors in Drosophila embryonic organ development

Ann S Hammonds1, Christopher A Bristow234, William W Fisher1, Richard Weiszmann1, Siqi Wu15, Volker Hartenstein6, Manolis Kellis23, Bin Yu5, Erwin Frise1 and Susan E Celniker1*

Author Affiliations

1 Department of Genome Dynamics, Division of Life Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

2 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

3 The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA

4 Current Address: Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA

5 Department of Statistics, University of California Berkeley, Berkeley, CA 94720, USA

6 Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA

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Genome Biology 2013, 14:R140  doi:10.1186/gb-2013-14-12-r140

Published: 20 December 2013

Additional files

Additional file 1: Table S1:

InterPro, Pfam, and hand curated DNA-binding domains used to generate the TF list used in these studies.

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Additional file 2: Table S2:

List of sequence-specific Drosophila TFs and their associated DNA binding domains. Columns A-D show the FlyBase identifiers, gene symbols, and synonyms for the 708 TF genes described in this study and their associated DNA binding domains (DBD). Shown in columns E and F are the corresponding FlyTF final calls and scores, or NA for genes not annotated as a TF in the FlyTF list of 754 putative TFs [59].

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Additional file 3: Table S3:

Correlation of controlled vocabulary terms, collapsed terms, and organ systems. Mapping of the names and abbreviations for CV (controlled vocabulary), CT (collapsed terms), and OS (organ system) and the stage ranges to which the terms apply are shown in adjacent columns. Abbreviations for CT terms (column D) are used in Figure 3. Terms that have no true organ system association (for example, ‘maternal’ and ‘ubiquitous’) are indicated by #N/A, but ubiquitous is arbitrarily assigned an organ system number of 17.

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Additional file 4: Figure S1:

Examples of TF expression patterns representing the 16 organ systems.

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Additional file 5: Table S4:

Expression category by stage range for all genes in this study. The ‘Gene set’ entry (column C) indicates whether the gene is from the list of 708 TFs (TF) or is from the remaining genes in the Release 3 BDGP expression pattern collection (non-TF). Expression classes are as described in Figure 1. The entry under ‘All stages’ (column D) is the summary classification for each TF and is used in the counts shown in Figure 1D. The separate classifications for each of the six stage ranges were used to determine the enrichment by stage shown in Figure 1E.

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Additional file 6: Table S5:

RNA-seq scores for the embyronic time course samples for each TF with stage-by-stage in situ expression pattern categories.

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Additional file 7: Figure S2:

Gene expression profiling of 25 TFs not detected spatially in embryos.

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Additional file 8: Table S6:

Expression matrix clustered by organ system. Following the TF gene name, FlyBase identifier, and DBD, columns record expression of each TF in each organ system by stage range. The organ system color code is shown in Figure 2 and the number of columns for each organ system reflects the number of stages where the organ system is morphologically detectable (Figure 2). Columns are ordered by organ system according to the organ system number code shown in Table S3 (Additional file 3). A colored box indicates expression and clicking on a colored box will show the number code for the organ system; clicking on a white box will show 0 for not expressed in that organ system at that stage. TFs (rows) are clustered by organ system (1 to 16) with black lines separating the organ system clusters. A TF will appear in a new row for every organ system where it is expressed. All TFs with patterned zygotic expression are included in the matrix. If a TF also shows ubiquitous staining at any stage, this is indicated by colored boxes in the five columns designated organ system 17, ubiquitous. Maternal staining (stages 1 to 3) is indicated by a single gray box with numerical code 18 in the last column of the matrix. In separate tabs, single organ system clusters are shown using numerical organ system codes without the color-coding.

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Additional file 9:

Supplemental text. Text descriptions of TF expression profiles for all 16 organ systems, detailed legends for supplemental figures, and supplemental references.

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Additional file 10: Figure S3:

SOM maps illustrating widely dispersed positions of TFs in three organ systems.

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Additional file 11: Figure S4:

Developmental dynamics of TFs expressed in the visual primordia organ system.

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Additional file 12: Table S7:

RNA-seq sample descriptions, accession numbers, and references.

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