Gutiérrez-Ríos Rosa-María:
 
  • Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.
Rosa María Gutierrez

1.The Bacillus subtilis TRN.

Appendix 1. Full TRN

The full B. subtilis TRN is available for download, in a format that facilitates network filtering based on the source (and reliability) of gene regulatory interactions. The meaning of the columns in this file is the following:

Column 1: Regulatory gene, traditional name;

Column 2: Target gene, traditional name;

Column 3: Regulatory function over target gene

Column 4: Target gene, GeneBank ID;

Column 5: Target gene, Locus Tag;

Appendix 2. Trasncription and sigma factor TRN.

The TF TRN of B. subtilis is available for download, in a format that facilitates network filtering based on the source (and reliability) of gene regulatory interactions. The meaning of the columns in this file is the following:

Column 1: Regulatory gene, traditional name or names.

Column 2: Target gene, traditional name or names.

 
  • Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli.
Rosa María Gutierrez, Julio Freyre, Osbaldo Resendis, Julio Collado, Milton Saier and Guillermo Gosset

 

 

     Table 1

Available information for the significant expressed genes. The columns shows in the following order: Functional modules, module name, submodule, gene identifier in the genome, gene name, name of the kwon or predicted operon, known promoter, transcription factors affecting the expressed genes, sigma factor, ratio of expression for the wtg vs. wt, log ratio of the wtg vs. wt, ratio of expression for the crp mutant vs. wt, log ratio of the crp mutant vs. wt, function of the gene product, Monica Riley’s functional class and operon type as known or predicted. The label N/A in the submodule column indicates that no submodules were found.

  • Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli.

Carlos Daniel Vázquez 1, Julio A Freyre-Gonzalez 1, Guillermo Gosset 2 and Rosa María Gutierrez-Ríos*1.

Table 2

Available information for the significant expressed genes on B. subtilis. The columns shows in the following order: Module number, submodule number, functional module, gene name, operon name, regulatory phrase,sigma factor, logarithmic level of expression (positive values indicated induction, negative values indicates repression),gene product function, Classification (as describe in Subtilist DB).

Figure 1

Figure1-supplementary material. A graphical representation of the regulatory subnetwok of B. subtilis growing in LB+G. Genes are represented as nodes connected by edges. Genes induced and repressed in the microarray are shown in red and green respectively. In pink we represent the regulatory genes with no significant level of expression. The figure shows a giant connected network and 12 disconnected subnetworks.


Tesis: Reconstrucción y estudio topológico de las redes de regulación y del metabolismo de Bacillus subtilis
Apéndices