Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

Transcriptional double-autorepression feedforward circuits act for multicellularity and nervous system development

Hisakazu Iwama1*, Koji Murao2, Hitomi Imachi2 and Toshihiko Ishida2

Author Affiliations

1 Life Science Research Center, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan

2 Division of Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan

For all author emails, please log on.

BMC Genomics 2011, 12:228  doi:10.1186/1471-2164-12-228

Published: 11 May 2011

Additional files

Additional file 1:

Preferred biological processes of the effecter genes targeted by each of the 13 TF-TF connections of DAR-FFCs. The overrepresented GO terms for biological processes are listed for each of the 13 TF-TF connections of DAR-FFCs.

Format: PDF Size: 70KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Genomic nucleotide sequences 8-kb upstream of the translation start site for 5169 pairs of human-mouse orthologs. The genomic nucleotide sequences 8-kb upstream of the translation start site are shown for 5169 pairs of human-mouse orthologs together with the corresponding gene symbols and gene IDs.

Format: ZIP Size: 11.4MB Download file

Open Data

Additional file 3:

Regulator mode annotations of the 82 TFs used to identify the TFBSs. The annotations of the regulator modes (repressor, activator or bimodal) are shown for the 82 TFs used in this study together with the Gene IDs and the annotation source.

Format: PDF Size: 72KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Alignments of conserved blocks for 5169 human-mouse orthologs with conserved TFBSs. The location and motif information for 386237 TFBSs are displayed in a character-based alignment-embedded layout. Each file name stands for a gene symbol and the file contains the alignments of conserved blocks with TFBS information for the corresponding gene. Each alignment is not interleaved. The graphical alignments with TFBS information for the 5169 human-mouse ortholog pairs are provided in a browsable format at our website http://genet.med.kagawa-u.ac.jp/pub/HMO_5169/List.htm webcite, together with the character-based alignments with TFBSs and raw sequences contained in Additional files 4 and 2 respectively.

Format: ZIP Size: 16.8MB Download file

Open Data

Additional file 5:

Transcriptional connection matrix M. The transcriptional targeting of the 82 TFs to the 5169 genes is shown as a matrix M in which Mij = 1 if TF j targets gene i and Mij = 0 in the absence of such targeting. Each TF i is designated with an official gene symbol in a column and each target gene j is designated by an NCBI Entrez Gene ID.

Format: CSV Size: 862KB Download file

Open Data