Computational protocol: Positional Cloning Reveals Strain-Dependent Expression of Trim16 to Alter Susceptibility to Bleomycin-Induced Pulmonary Fibrosis in Mice

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Protocol publication

[…] Putative transcription factor binding sites located within the 1.4 kb of the promoter region were identified in silico using the PROMO program , and TFsearch (v.1.3) of the TRANSFAC database with a focus on murine specific transcription factors and transcription factor binding sites. The sequence was also analyzed with the MATCH public 1.0 algorithm by Biobase GmbH using vertebrate weight matrices and a minimum false negative profile.In order to determine evolutionary conservation of promoter region B6/C3H SNPs or deletions we used the Multiz Alignment & Conservation algorithm of the UCSC genome browser (http://genome.ucsc.edu; ). The graphic output was created using CodonCode Aligner (v. 3.7.1, Codon Code Corporation). […]

Pipeline specifications

Software tools PROMO, TFSearch, Biobase, CodonCode Aligner
Databases TRANSFAC UCSC Genome Browser
Applications Miscellaneous, Genome data visualization
Organisms Mus musculus
Diseases Lung Diseases, Pulmonary Fibrosis
Chemicals Bleomycin