Sentence examples for database matrices from inspiring English sources
The database matrices are divided into categories depending on their length.
Importantly, 16 of these genes contain MYC binding sites at their promoters based on TRANSFAC (eukaryotes transcription factors database) matrices [ 33].
Screening of the LXR peak sequences with all 459 non-redundant JASPAR database matrices (JASPAR core, version 10/2009), without DR4-type LXR RE among them, resulted in the following five most frequent motifs in the T09-treated sample (with similarity P < 10-4): EWSR1-FLI1 (15.4%), KLF4 (13.7%), RREB1 (13.7%), SP1 (13.1%) and the DR1-type RE PPARG RXR (12.0%).
The spectra were interpreted with Analyst QS software (Applied Biosystems, Applera Deutschland GmbH, Darmstadt, Germany) and MASCOT database (Matrix Science Ltd., London, UK).
We further identified a putative p53 DNA-binding site in the NOS3 promoter region (Fig 2A) using bioinformatics analysis of MatInspector genomatix database (matrix sim; score >0.9).
Single TFBSs were predicted in these regulatory regions using known binding site motifs as stored in the TRANSFAC database (matrix and core similarity values of 0.85 and 0.95 were employed) [ 58].
The raw data files were transformed to the mzData format using the Proteome Discoverer (ThermoFisher) tool and peptide identifications were performed using the MASCOT database (Matrix Science, London, UK).
The TRANSFAC database matrix identifier The colloquial name of the protein that binds the TFBS along with its official HUGO name in parentheses There are numerous experimentally characterized TFBS in the human genome (7 10%) that are derived from repetitive DNA indicating a pronounced effect of repetitive DNA on human gene regulation.
In order to show the relative diversity of actives towards inactives randomly selected from the ZINC database, the matrices of Tanimoto coefficients were calculated (see Additional file 1: Figure S1).
We first investigated how trivial it was to bypass the blocked reactions using reactions from the KEGG database (U matrix).
The open-access JASPAR database of matrix-based transcription factor binding profiles (Bryne et al. 2008) was used to search 3,000 bp upstream and 500 bp downstream of the TSS of each gene.
