scholarly journals Functional transcription factor target discovery via compendia of binding and expression profiles

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Christopher J. Banks ◽  
Anagha Joshi ◽  
Tom Michoel
Keyword(s):  
Transcription Factor ◽  
Expression Profiles ◽  
Target Discovery ◽  
Transcription Factor Target ◽  
Functional Transcription Factor

scholarly journals TARGET: A Transient Transformation System for Genome-Wide Transcription Factor Target Discovery

2013 ◽  
Vol 6 (3) ◽  
pp. 978-980 ◽  
Author(s):  
Bastiaan O.R. Bargmann ◽  
Amy Marshall-Colon ◽  
Idan Efroni ◽  
Sandrine Ruffel ◽  
Kenneth D. Birnbaum ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transient Transformation ◽  
Transformation System ◽  
Target Discovery ◽  
Genome Wide ◽  
Transcription Factor Target

scholarly journals Identification and characteristic analysis of enhancers across 13 major cancer types

2021 ◽  
Author(s):  
Mingming Qian ◽  
Wenzhu Wang ◽  
Yana Zhang ◽  
Yi Zhao ◽  
Huige Quan ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Sites ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Characteristic Analysis ◽  
Cancer Types ◽  
Highly Correlated ◽  
Functional Transcription Factor

Abstract Enhancers are often mutated and dysregulated in various diseases such as cancer. By integrating the FANTOM enhancers expression profiles and RNA-seq data from TCGA of 13 cancers and their corresponding para-cancerous tissues, we systematically identified a total of 4702 significantly differentially expressed enhancers (DE enhancers). Furthermore, a total of 1036 differentially expressed genes (DE genes) regulated by differentially expressed enhancers (DE enhancers) were identified. It was found that in these 13 cancers, most (61.13%) enhancers were ubiquitously expressed, whereas DE enhancers were more likely to be tissue-specific expressed, and the DE genes regulated by DE enhancers were significantly enriched in cancer-related pathways. Finally, it was manifested that 74 SNPs located in 37 DE enhancers, and these SNPs affected the gain and loss of functional transcription factor binding sites (TFBS) of 758 transcription factors, which had been shown to be highly correlated with tumorigenesis and development.

Analysis of steric effects in DamID profiling of transcription factor target genes

Genomics ◽  
2017 ◽  
Vol 109 (2) ◽  
pp. 75-82 ◽  
Author(s):  
Mirana Ramialison ◽  
Ashley J. Waardenberg ◽  
Nicole Schonrock ◽  
Tram Doan ◽  
Danielle de Jong ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Steric Effects ◽  
Transcription Factor Target

scholarly journals Sex- and Tissue-Specific Functions of Drosophila Doublesex Transcription Factor Target Genes

2014 ◽  
Vol 31 (6) ◽  
pp. 761-773 ◽  
Author(s):  
Emily Clough ◽  
Erin Jimenez ◽  
Yoo-Ah Kim ◽  
Cale Whitworth ◽  
Megan C. Neville ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Tissue Specific ◽  
Transcription Factor Target

Chicken vitellogenin gene-binding protein, a leucine zipper transcription factor that binds to an important control element in the chicken vitellogenin II promoter, is related to rat DBP

1991 ◽  
Vol 11 (10) ◽  
pp. 4863-4875
Author(s):  
S V Iyer ◽  
D L Davis ◽  
S N Seal ◽  
J B Burch
Keyword(s):  
Transcription Factor ◽  
Binding Site ◽  
Binding Protein ◽  
Expression Profiles ◽  
Control Element ◽  
Cdna Expression Library ◽  
Leucine Zippers ◽  
Expression Library ◽  
Positive Elements ◽  
Vitellogenin Gene

We screened a chicken liver cDNA expression library with a probe spanning the distal region of the chicken vitellogenin II (VTGII) gene promoter and isolated clones for a transcription factor that we have named VBP (for vitellogenin gene-binding protein). VBP binds to one of the most important positive elements in the VTGII promoter and appears to play a pivotal role in the estrogen-dependent regulation of this gene. The protein sequence of VBP was deduced from a nearly full length cDNA copy and was found to contain a basic/zipper (bZIP) motif. As expected for a bZIP factor, VBP binds to its target DNA site as a dimer. Moreover, VBP is a stable dimer free in solution. A data base search revealed that VBP is related to rat DBP. However, despite the fact that the basic/hinge regions of VBP and DBP differ at only three amino acid positions, the DBP binding site in the rat albumin promoter is a relatively poor binding site for VBP. Thus, the optimal binding sites for VBP and DBP may be distinct. Similarities between the VBP and DBP leucine zippers are largely confined to only four of the seven helical spokes. Nevertheless, these leucine zippers are functionally compatible and appear to define a novel subfamily. In contrast to the bZIP regions, other portions of VBP and DBP are markedly different, as are the expression profiles for these two genes. In particular, expression of the VBP gene commences early in liver ontogeny and is not subject to circadian control.

scholarly journals Thyrotroph embryonic factor (TEF) is differentially expressed in high-grade serous ovarian cancers.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Ovarian Cancer ◽  
Transcription Factor ◽  
Differential Expression ◽  
Expression Profiles ◽  
Gynecologic Cancer ◽  
Bzip Transcription Factor ◽  
High Grade ◽  
Significant Differential Expression ◽  
Primary Tumors ◽  
Embryonic Factor

Ovarian cancer is the most lethal gynecologic cancer (1). We sought to identify genes associated with high-grade serous ovarian cancer (HGSC) by comparing global gene expression profiles of normal ovary with that of primary tumors from women diagnosed with HGSC using published microarray data (2, 3). We previously reported differential expression of the PAR-bZIP transcription factor HLF in HGSC (4). Here, we report significant differential expression of a second PAR-bZIP transcription factor, thyrotroph embryonic factor (TEF) (5) in high-grade serous ovarian tumors.

scholarly journals Transcriptomic profile of Pea3 family members reveal regulatory codes for axon outgrowth and neuronal connection specificity

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Başak Kandemir ◽  
Gizem Gulfidan ◽  
Kazim Yalcin Arga ◽  
Bayram Yilmaz ◽  
Isil Aksan Kurnaz
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Neural Circuit ◽  
Molecular Model ◽  
Expression Profiles ◽  
Neuroblastoma Cells ◽  
Branching Morphogenesis ◽  
Subfamily Member ◽  
Circuit Formation ◽  
Cell Cell

Abstract PEA3 transcription factor subfamily is present in a variety of tissues with branching morphogenesis, and play a particularly significant role in neural circuit formation and specificity. Many target genes in axon guidance and cell–cell adhesion pathways have been identified for Pea3 transcription factor (but not for Erm or Er81); however it was not so far clear whether all Pea3 subfamily members regulate same target genes, or whether there are unique targets for each subfamily member that help explain the exclusivity and specificity of these proteins in neuronal circuit formation. In this study, using transcriptomics and qPCR analyses in SH-SY5Y neuroblastoma cells, hypothalamic and hippocampal cell line, we have identified cell type-specific and subfamily member-specific targets for PEA3 transcription factor subfamily. While Pea3 upregulates transcription of Sema3D and represses Sema5B, for example, Erm and Er81 upregulate Sema5A and Er81 regulates Unc5C and Sema4G while repressing EFNB3 in SH-SY5Y neuroblastoma cells. We furthermore present a molecular model of how unique sites within the ETS domain of each family member can help recognize specific target motifs. Such cell-context and member-specific combinatorial expression profiles help identify cell–cell and cell-extracellular matrix communication networks and how they establish specific connections.

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