Computational protocol: Identification and characterization of the novel Col10a1 regulatory mechanism during chondrocyte hypertrophic differentiation

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Protocol publication

[…] The 150-bp Col10a1 enhancer (−4296 to −4147 bp) was subjected to in silico sequence analysis to search for TFBS using following web-based programs: (1) TFSEARCH: the TFSEARCH tool was used to search for potential TFBS with a cutoff score of 85., The web address for TFSEARCH is at http://www.cbrc.jp/research/db/TFSEARCH.html. (2) Promo 3.0: Promo uses the TRANSFAC database (version 8.3) to identify TFBS in a given DNA sequence., The web address can be accessed at http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3. The searching result of potential TFBS will be displayed through a graphical interface or as a downloadable text file. (3) Transcription factor affinity prediction (TRAP): TRAP is used to predict which TFs are susceptible to bind a promoter with highest affinity. TRAP uses the TRANSFAC database and the searching result is listed in a table ranking the affinity of TFs with a P-value. TRAP is available at http://trap.molgen.mpg.de/cgi-bin/home.cgi. (4) MATCH: Match is a weight matrix-based program for predicting TFBS., With a courtesy of BIOBASE, we were able to use the TRANSFAC Professional database (version 10.1, January 2013). The address is at http://www.biobase-international.com/product/transcription-factor-binding-sites. […]

Pipeline specifications

Software tools TFSearch, PROMO, TRAP, Biobase
Databases TRANSFAC
Application Miscellaneous
Organisms Mus musculus, Homo sapiens, Saccharomyces cerevisiae
Diseases Osteoarthritis