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Quantifying the regulatory role of individual transcription factors in Escherichia coli

• Authors : Guharajan, Sunil; Chhabra, Shivani; Parisutham, Vinuselvi ...

Subjects: gene regulation; quantitative modeling; synthetic biology

• Source: Cell reports ; 37 ; 6 ; 109952 ; United States

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Quantifying the regulatory role of individual transcription factors in Escherichia coli [preprint]

• Authors : Guharajan, Sunil; Chhabra, Shivani; Parisutham, Vinuselvi ...

Subjects: Systems Biology; Transcription factors; Escherichia coli

• Source: bioRxiv

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Quantifying the regulatory role of individual transcription factors in Escherichia coli

• Authors : Guharajan, Sunil; Chhabra, Shivani; Parisutham, Vinuselvi ...

• Source: Cell Reports ; volume 37, issue 6, page 109952 ; ISSN 2211-1247

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Nanopore sensing of individual transcription factors bound to DNA

• Authors : Squires, Allison; Atas, Evrim; Meller, Amit

• Source: Scientific Reports ; volume 5, issue 1 ; ISSN 2045-2322

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Imaging individual transcription factors

• Authors : Williams, Ruth

• Source: The Journal of Cell Biology ; volume 177, issue 6, page 946a-946a ; ISSN 1540-8140 0021-9525

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Additional file 1 of Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity

• Authors : B. Zhou (2956527); T. R. Stueve (11853345); E. A. Mihalakakos (11853348)

Subjects: Medicine; Cell Biology; Genetics

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Figure 6. MR1T cell clones exhibit divergent transcriptional responses to antigen stimulation. ; Betweeness centrality analysis illustrating the key transcription factors that were differentially expressed in resting (No Ag) and antigen-activated (Ag Act) MR1T cell clones (A) DGB129 and (B) DGB70. Color code represents betweeness centrality score. The size of the nodes (or hubs) indicates the relative importance of individual transcription factors within the whole gene network. (C) Heat-map comparing key transcription factors that were differentially expressed in resting (Rest.) and antigen-activated (Act.) DGB129 and DGB70 MR1T cell clones (analysis performed by PageRank algorithm).

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Figure 3. LgPCA points to master regulators of human organogenesis and the causes of human congenital disorders. ; (a) Predicted regulation by iRegulon (Janky et al., 2014) of the most extreme 1000 genes for different PCs identifies known and unexpected transcription factors regulating human organogenesis. In several examples, individual transcription factors (e.g. REST, NR5A1, HNF4A, FOXA1 and SRF) were predicted to regulate nearly half of the most extreme 1000 genes. (b) Transcription factors at the extremes of individual PCs in the LgPCA are responsible for a diverse range of congenital disorders (red names in the ovals for heart and testis; full details in Supplementary file 1G). To validate the utility of these data, we conservatively selected some of the earliest critical regions for these disorders (two ‘Proven’ examples on the left; all 53 listed in Supplementary file 1H). LgPCA frequently isolated the correct transcription factor from an average of 111 genes across >10 Mb, shown for NKX2-5 in congenital heart disease and SOX9 in campomelic dysplasia. Beyond this validation LgPCA similarly predicts causative transcription factors (blue) for many unresolved congenital disorders such as developmental heart abnormalities in Chr1p36 deletion syndrome and sex reversal / disorders of sex differentiation (DSD) (all 13 examples in Supplementary file 1H).

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Regulatory insight for a Zn2Cys6 transcription factor controlling effector-mediated virulence in a fungal pathogen of wheat.

• Authors : John, Evan¹ (AUTHOR) ; Verdonk, Callum¹ (AUTHOR); Singh, Karam B.^1,2 (AUTHOR)

• Source: PLoS Pathogens. 9/23/2024, Vol. 20 Issue 9, p1-23. 23p.

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Brahmachary et al. Computational Promoter Analysis of Mouse, Rat and Human Antimicrobial Peptide-coding Genes Supplementary Table 6. Distribution of individual transcription factors among AMP families Transcription No. AMP

• Authors : The Pennsylvania State University CiteSeerX Archives

Subjects: mbp; secretogranin; spyy

• Source: http://www.biomedcentral.com/content/supplementary/1471-2105-7-s5-s8-s6.pdf.

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