Abstract
BackgroundGenes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental processes. Transcription factors control the expression of their downstream target genes by interacting with cis-regulatory elements. Maternal factors initiate embryonic developmental programs by regulating the expression of zygotic genes and various other events during early embryogenesis.ResultsThis article documents the transcription factors of 77 metazoan species as well as human and mouse maternal factors. We improved the previous method using a statistical approach adding Gene Ontology information to Pfam based identification of transcription factors. This method detects previously un-discovered transcription factors. The novel features of this database are: (1) It includes both transcription factors and maternal factors, although the number of species, in which maternal factors are listed, is limited at the moment. (2) Ontological representation at the cell, tissue, organ, and system levels has been specially designed to facilitate development studies. This is the unique feature in our database and is not available in other transcription factor databases.ConclusionsA user-friendly web interface, REGULATOR (http://www.bioinformatics.org/regulator/), which can help researchers to efficiently identify, validate, and visualize the data analyzed in this study, are provided. Using this web interface, users can browse, search, and download detailed information on species of interest, genes, transcription factor families, or developmental ontology terms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0552-x) contains supplementary material, which is available to authorized users.
Highlights
Genes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental processes
A user-friendly web interface, REGULATOR, which can help researchers to efficiently identify, validate, and visualize the data analyzed in this study, are provided
All proteins were categorized into four groups, and features that are well represented in each group were selected using feature selection
Summary
Genes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental processes. Maternal factors initiate embryonic developmental programs by regulating the expression of zygotic genes and various other events during early embryogenesis. Transcription factors (TFs) bind to the cis-regulatory elements of downstream target genes and promote or block the recruitment of RNA polymerase II to those promoter regions [1,2]. They control various developmental processes by regulating cell fate specification [3,4], morphogenesis [5,6], the cell cycle [7], apoptosis [8] and pathogenesis [9]. More intelligent methods are needed in order to facilitate better prediction
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