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Publications for TRANSFAC
Systematic pan cancer analysis of somatic allele frequency
[…] nnotation147/index.jsp). Pathogenicity was modeled using PolyPhen, CADD and FATHMM methods, and conservation was assessed based on GERP scores–. Transcription factor binding sites were analyzed using TRANSFAC 7.0. […]
Exosome markers associated with immune activation and oxidative stress in HIV patients on antiretroviral therapy
[…] base (www.exocarta.org) and the top 200 most abundant plasma proteins published previously. Functional annotation was performed by GO mapping using PANTHER (pantherdb.org) and Biobase (genexplain.com/transfac). […]
Development of a computational promoter with highly efficient expression in tumors
[…] overexpress transgenes in the growing tumor area. Therefore, we designed the sequence of this promoter by bioinformatics. Figure displays the flow chart describing the study design. According to the TRANSFAC database, 1624 genes with TF activity were identified. Subsequently, the Gene Ontology Consortium was used to define whether the activity of these TFs was associated with cell growth. Since a […]
Selection on the regulation of sympathetic nervous activity in humans and chimpanzees
[…] We searched the DHS2 sequences for transcription factor binding sites on the basis of the TRANSFAC [–] and JASPAR [–] databases by running FIMO  at the P value threshold of 10-3. Our motif search was performed for the reference human and chimpanzee genomes (hg19 and panTro4) that carried […]
Induction of muscle stem cell quiescence by the secreted niche factor Oncostatin M
[…] 01A, SA Bioscience) designed for quantitative RT-PCR analysis were used to amplify the putative Stat3 binding site adjacent to the mouse Pax7 locus (Chr4: 139387970-139388390), identified via Biobase Transfac analysis (Biobase Corp. MA). The Stat3 occupancy was calculated as a ratio of the amplification efficiency of Stat3 ChIP over input chromatin. […]
Synergistic co regulation and competition by a SOX9 GLI FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions
[…] ing DNA elements. The Position Weight Matrices used for identification of SOX9 dimer and GLI binding elements were constructed from the SOX9 binding HMG core sequence and the GLI binding consensus in TRANSFAC database respectively. […]
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