Software
TFCat: the curated catalog of mouse and human transcription factors
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* Corresponding author: Rob Sladek robert.sladek@mcgill.ca
- † Equal contributors
1 Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics - Child and Family Research Institute, University of British Columbia, West 28th Avenue, Vancouver, V5Z 4H4, Canada
2 Departments of Medicine and Human Genetics, McGill University and Genome Quebec Innovation Centre, Dr. Penfield Avenue, Montreal, H3A 1A4, Canada
3 Banting and Best Department of Medical Research, University of Toronto, College Street, Toronto, M5S 3E1, Canada
4 Center for Developmental Therapeutics, Seattle Children's Research Institute, Olive Way, Seattle, 98101, USA
Genome Biology 2009, 10:R29 doi:10.1186/gb-2009-10-3-r29
Published: 12 March 2009Additional files
Additional data file 1:
Table S1: gene annotation judgment summary counts from the quality assurance assessment process. Table S2: quality assurance gene pair judgment annotations. Table S3: independent annotations of TFs when the same PubMed evidence was used. Table S4: PFAM and Superfamily group model DBD predictions for the annotated TF genes. Table S5: DNA-binding classification extensions added to the Luscombe et al. [15] classification system. Table S6: protein class counts of genes predicted to contain multiple instances of the same DBD. Table S7: DNA-binding TFs predicted to contain two different DNA-binding classes. Table S8: DNA-binding TFs that do not contain a detected DBD. Table S9: DNA-binding TFs with no detected protein family-level domain. Table S10: annotated single-stranded DNA-binding TFs. Table S11: summary of the counts enumerated in the TFCat comparison with GO. Table S12: summary of the counts enumerated in the comparison of TFCat classified HMM DBDs with the DBD database (DBDdb). Table S13: Superfamily DBD comparisons with DBDdb. Table S14: PFAM DBD comparisons with DBDdb. Table S15: Fox family test set genes. Table S16: Sox family test set genes. Figure S1: Venn diagram of the overlap of the four initial TF datasets. Figure S2: plots for the analysis of cluster pruning methods using the Fox test set. Figure S3: plots for the analysis of cluster pruning methods using the Sox test set. Figure S4: TFCat annotation workflow implementation. Figure S5: screen shots of the backend web-based TFCat annotation tool. Figure S6: Sox-containing cluster membership for the evaluated cluster pruning methods. Figure S7: Fox-containing cluster membership for the evaluated cluster pruning methods. Figure S8: an example of pruned Fox-containing clusters generated using the I's only method using a threshold of 0.21.
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