Bioinformation and molecule of the month: Multiple interactive pathways for a single gene, NFkB

This Editorial is divided into two parts. 1. A summary of what is under the Bioinformation aegis; 2. An example of a highly networked gene, NF-kB.

The Bioinformation Aegis

Bioinformation (Online ISSN 0973-2063; Print ISSN 0973-8894) is a peer-reviewed journal that grows in leaps and bounds as the global scientific endeavor advances. Bioinformation publishes original biological research that utilizes mathematical and computational analysis. The fields in such analyses range from biochemistry and cell biology to genetics, epigenetics, systems biology, and brain imaging, from agriculture to tissue engineering and transplantation, from nanotechnology to evolution, and from basic research to clinical medicine, infectious disease, immunology, molecular structure, molecular therapy, and vaccines. This work is further often analyzed from the vantage point of data cleaning, analysis, representation, storage, retrieval, and knowledge extraction. Developing databases, datasets, prediction models, and computer programs fall under the purview of Bioinformation as well. Research articles published in Bioinformation demonstrate novelty, relevance, and coherence.

Global scientific advances are accelerating, research and clinical studies are expanding, topics of study are increasing, as are publications, journals, and books. E-publishing has participated in this intellectual revolution, and has widened the already expanding scope and reach. Moreover, novel fields increase contemporaneously, e.g. nanotechnology and nanomedicine, imaging and genetics, vaccines for cancer, microorganisms (e.g. bacteria and parasites), and viruses (e.g. HIV, HCV, HBV, and arboviruses), as well as genetic engineering. Genetic engineering in agriculture is ubiquitous; genetic engineering in humans and animals is in progress. All this work requires concomitant development of fields including bioinformatics and modes of analysis. It is among the goals of Bioinformation to continue to promote and be the venue of all these advances and improvements.

NF-kB, a highly networked gene

The example selected for this Editorial is the gene, NF-kB (Nuclear Factor kappa-light-chain-enhancer of activated B cells). NF-kB is a central gene that is expressed in eukaryotic cells. It is a transcription factor and interacts with the promoters and gene products of many gene pathways. Thus, it is central in gene control and expression and is highly utilized throughout eukaryotic evolution. It is important, for example, for treatment of cancer and due to its function in immunology. It is also involved in the control of expression of many mammalian viruses. More than 12 years ago, a list was published of some 114 genes with which NF-kB interacts. Please see Table 1 (see supplementary material). A current view extends the interactions of NF-kB including 99 genes as indicated in (Figure Figure 1).

Figure 1.

NF-kB interactions. In this figure, interactions - linecolor are Regulation- beige, Co-expression - purple and Physical interaction-brown. (GenePro SA Biosciences, http://www.sabiosciences.com/) http://www.panomics.com/ NFkBhuman.htm

Table 1 (see supplementary material) lists descriptions and functions of genes in that table. As noted in the (Figure 1) legend, interactions of NF-kB are indicated that involve regulation, co-expression, and actual physical interaction. Molecular processes in this figure include apoptosis, immunology, transcription, chromatin, and regulation of the NF-kB gene itself. Additional interactions are not shown because of the excessive overlapping information that would result in the figure. These include down-regulation, upregulation, predicted protein interaction, and predicted transcription factor interactions. Similarly, only 100 genes are shown since more than that would make the figure illegible.

In summary then, this journal,Bioinformation, has a wide array of bioinformatics in its purview. This Editorial provides a simple scenario of the complexity of molecular information available, already in the literature, even for a single molecule.