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Pipeline publication

[…] set of all human GO terms (expected) using the χ2 test, or the Fisher's exact test is the expected value<5. The Benjamini False Discovery Rate correction for multiple testing was used to adjust the resulting P-values. GO annotation terms that were found to be overrepresented in two or more different clusters were chosen for further analysis. Individual gene functions were explored using the NCBI Entrez Gene database . The graphical (parent-child) relationships among GO terms related to immune response were characterized using the GeneInfoViz program []. GO term significance levels were color coded using the program matrix2png []., Conserved hg17 genomic sites were characterized using the phastCons program []. Alignment, using blastz [] and multiz [], and comparison among 17 vertebrate genome sequences were used to characterize conserved sites. The genome coordinates for conserved sites were retrieved from the table named phastConsElements17way. Absolute differences between the relative levels of CD4+ T cell expression were calculated for human and mouse orthologous genes pairs described previously []. The evolutionary divergence between human and mouse orthologous proteins was measured as the number of substitutions per site using the Poisson Correction distance []., Wolfgang J. Miller, Laboratories of Genome Dynamics, Center of Anatomy and Cell Biology, Medical University of Vienna, Austria (nominated by Jerzy Jurka, Genetic […]

Pipeline specifications

Software tools PHAST, LASTZ, TBA
Organisms Homo sapiens, Mus musculus
Diseases Drug Hypersensitivity, Neoplasms, Sexually Transmitted Diseases, Viral, Retroviridae Infections, HIV Infections