Open Access Highly Accessed Research

Analysis of variation at transcription factor binding sites in Drosophila and humans

Mikhail Spivakov12*, Junaid Akhtar2, Pouya Kheradpour34, Kathryn Beal1, Charles Girardot2, Gautier Koscielny1, Javier Herrero1, Manolis Kellis34, Eileen EM Furlong2 and Ewan Birney1*

Author Affiliations

1 European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK

2 Genome Biol Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany

3 MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA

4 Broad Institute, Cambridge, MA 02142, USA

For all author emails, please log on.

Genome Biology 2012, 13:R49  doi:10.1186/gb-2012-13-9-r49

Published: 5 September 2012

Additional files

Additional file 1:

Supplementary figures S1 to S7 and Supplementary note. Figure S1: individual variation of bound and unbound Twi, Bin and Tin motifs. Figure S2: relationship between cross-species variation and information content at Twi, Bin and Tin motifs. Figure S3: general distributions of TFBS load in Drosophila and human. Figure S4: additional information for the analysis of TFBS load relative to PWM match score. Figure S5: distributions of TFBS load along Drosophila chromosome arms. Figure S6: additional information on the per-individual analysis of CTCF binding. Figure S7: naturally occurring mutations at mesodermal TFBSs do not affect in vitro CRM activity. Supplementary note: selection of TF binding motifs for the analysis.

Format: PDF Size: 929KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Tables S1 and S2. A two-sheet Excel file listing the properties of Drosophila (Table S1) and human (Table S2) TFs included in this study.

Format: XLS Size: 925KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Drosophila TFBS instances included in this study and their variation properties. A plain text table listing the position, sequence, PWM match score, branch length score (BLS), mutational load (L), distance from the nearest TSS and, when detected, the count and PWM score of the alternative allele for Drosophila TFBSs included in this study.

Format: TXT Size: 2.2MB Download file

Open Data

Additional file 4:

Human TFBS instances included in this study and their variation properties. A plain text table listing the position, sequence, PWM match score, branch length score (BLS), mutational load (L), distance from the nearest TSS and, when detected, the count and PWM score of the alternative allele for human TFBSs included in this study.

Format: TXT Size: 6.6MB Download file

Open Data

Additional file 5:

CTCF binding and TFBS variation properties for four individuals from McDaniell et al. A plain text table listing the position, sequence properties and ChIP binding signals at CTCF binding sites with detected variation in four individuals from [16].

Format: TXT Size: 112KB Download file

Open Data

Additional file 6:

CTCF binding and TFBS variation properties for three individuals from Maurano et al. A plain text table listing the position, sequence properties and ChIP binding signals at CTCF binding sites with detected variation in three individuals from [44].

Format: TXT Size: 81KB Download file

Open Data