CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis.

BACKGROUND: Finding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining. RESULTS: Here, we developed the R package "CeTF" that integrates the Partial Correlation with Information Theory (PCIT) and Regulatory Impact Factors (RIF) algorithms applied to gene expression data from microarray, RNA-seq, or single-cell RNA-seq platforms. This approach allows identifying the transcription factors most likely to regulate a given network in different biological systems - for example, regulation of gene pathways in tumor stromal cells and tumor cells of the same tumor. This pipeline can be easily integrated into the high-throughput analysis. To demonstrate the CeTF package application, we analyzed gastric cancer RNA-seq data obtained from TCGA (The Cancer Genome Atlas) and found the HOXB3 gene as the second most relevant TFs with a high regulatory impact (TFs-HRi) regulating gene pathways in the cell cycle. CONCLUSION: This preliminary finding shows the potential of CeTF to list master regulators of gene networks. CeTF was designed as a user-friendly tool that provides many highly automated functions without requiring the user to perform many complicated processes. It is available on Bioconductor ( http://bioconductor.org/packages/CeTF ) and GitHub ( http://github.com/cbiagii/CeTF ).

Imbalanced testicular metabolism induced by thyroid disorders: New evidences from quantitative proteome.

Thyroid dysfunctions, such as hypothyroidism and hyperthyroidism, are the second most prevalent endocrinopathies and are associated to reproductive disorders in men. Several genes are differentially modulated by thyroid hormones in testes and imbalances in thyroid hormone levels are also associated to alterations on sperm functionality. Imbalances on antioxidant defense mechanism and stress oxidative have been pointed out as the main factors for the impairments on male reproductive function. To clarify this issue, we investigated the expression and activity of antioxidant enzymes in testis, followed by their proteomic profile in attempt to characterize the mechanisms involved in the alterations induced by hypo- or hyperthyroidism in adult male rats. Hypothyroidism reduced the Gsr transcript expression and the activity of CAT and GSR enzymes, while the hyperthyroidism reduced the Gpx4 var2 transcript expression. Among 1082 identified proteins, 123 and 37 proteins were downregulated by hypothyroidism compared to euthyroid and hyperthyroid condition, respectively, being 36 proteins commonly reduced in both comparisons and one exclusively in hypo-hyperthyroidism comparison. A network containing 29 nodes and 68 edges was obtained in protein-protein interaction analysis and the functional enrichment analysis of differentially expressed proteins revealed significant alterations for several functions in hypo-euthyroid and hypo-hyperthyroid comparisons, such as ATP metabolic process, coenzyme binding, sperm part, peroxiredoxin activity, mitochondrial protein complex, intramolecular oxidoreductase activity, binding of sperm to zona pellucida, glutathione transferase activity, response to testosterone. Thus, there is a correlation between thyroid disorders and impaired antioxidant defense mechanism, resulting in reproductive dysfunctions, as infertility, mainly observed in hypothyroidism.