RPN4/YDL020C Literature Guide Help

Other names published for RPN4: SON1, UFD5, YDL020C

RPN4 - Computational analysis (24)

ReferenceOther Genes Addressed
Chang DT, et al.  (2012) A study on promoter characteristics of head-to-head genes in Saccharomyces cerevisiae. BMC Genomics 13 Suppl 1():S11
Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76
Brohee S, et al.  (2011) Unraveling networks of co-regulated genes on the sole basis of genome sequences. Nucleic Acids Res 39(15):6340-58
Calcada D, et al.  (2011) Quantitative modeling of the Saccharomyces cerevisiae flr1 regulatory network using an s-system formalism. J Bioinform Comput Biol 9(5):613-30
Erb I and van Nimwegen E  (2011) Transcription factor binding site positioning in yeast: proximal promoter motifs characterize tata-less promoters. PLoS One 6(9):e24279
Gordan R, et al.  (2011) Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol 12(12):R125
Monteiro PT, et al.  (2011) Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae. IET Syst Biol 5(5):308
Babbitt GA  (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8
Bailly-Bechet M, et al.  (2010) Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach. BMC Bioinformatics 11():355
Katebi AR, et al.  (2010) Structural interpretation of protein-protein interaction network. BMC Struct Biol 10 Suppl 1():S4
Morris RT, et al.  (2010) Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae. Bioinformatics 26(2):168-74
Chen T and Li F  (2009) Identifying cell cycle regulators and combinatorial interactions among transcription factors with microarray data and ChIP-chip data. Int J Bioinform Res Appl 5(6):625-46
Jothi R, et al.  (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294
Wu WS and Chen BS  (2009) Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. Bioinform Biol Insights 1():137-45
Lu CC, et al.  (2008) Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics 9 Suppl 12:S7
Ernst J, et al.  (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3():74
Laribee RN, et al.  (2007) CCR4/NOT complex associates with the proteasome and regulates histone methylation. Proc Natl Acad Sci U S A 104(14):5836-41
Steigele S, et al.  (2007) Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. BMC Biol 5:25
Tan K, et al.  (2007) Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A 104(4):1283-8
Workman CT, et al.  (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-9
Yu H and Gerstein M  (2006) Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A 103(40):14724-31
Yu T and Li KC  (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8
Haugen AC, et al.  (2004) Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol 5(12):R95
Hughes JD, et al.  (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296(5):1205-14