Wed, 20 Aug 2008 21:25:59 BST CiteULike: neils's matrix http://www.citeulike.org/user/neils/tag/matrix CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/767961 <i>Comput. Appl. Biosci., Vol. 12, No. 5. (1 October 1996), pp. 431-439.</i><br /><br />MOTIVATION: To improve the detection of nucleotide sequence signals (e.g. promoter elements) by position-weight matrices (PWM) using the concept of statistically significant matches. RESULTS: The Mksite program was originally developed for analyzing protein sequences. We report NMksite, a new version adapted to the processing of nucleotide sequences. NMksite creates PWM from nucleotide sequence block alignments or occurrence tables using three weight computation schemes. An original feature of NMksite is the numerical computation of the statistical significance of PWM matches. The utility of this concept is demonstrated in the context of the prediction of splice sites and promoter regions. AVAILABILITY: Mksite and other components of the MODEST (Motif DEsign and Search Tool) package (written in C/Unix) are available at http://igs-server.cnrs-mrs.fr CONTACT: E-mail: jmc@igs.cnrs-mrs.fr 10.1093/bioinformatics/12.5.431 The statistical significance of nucleotide position-weight matrix matches Jean-Michel Claverie Stephane Audic doi:10.1093/bioinformatics/12.5.431 Comput. Appl. Biosci., Vol. 12, No. 5. (1 October 1996), pp. 431-439. 2006-07-21T07:19:55-00:00 1996 Comput. Appl. Biosci. 12 5 431 439 bioinformatics matrix nucleotide pwm statistics http://www.citeulike.org/user/neils/article/2054455 <i>Mol Cell Biol, Vol. 23, No. 14. (Jul 2003), pp. 4796-4804.</i><br /><br />Stimulation of the Ras/extracellular signal-regulated kinase (ERK) pathway can modulate cell growth, proliferation, survival, and motility. The p90 ribosomal S6 kinases (RSKs) comprise a family of serine/threonine kinases that lie at the terminus of the ERK pathway. Efficient RSK activation by ERK requires its interaction through a docking site located near the C terminus of RSK, but the regulation of this interaction remains unknown. In this report we show that RSK1 and ERK1/2 form a complex in quiescent HEK293 cells that transiently dissociates upon mitogen stimulation. Complex dissociation requires phosphorylation of RSK1 serine 749, which is a mitogen-regulated phosphorylation site located near the ERK docking site. Using recombinant RSK1 proteins, we find that serine 749 is phosphorylated by the N-terminal kinase domain of RSK1 in vitro, suggesting that ERK1/2 dissociation is mediated through RSK1 autophosphorylation of this residue. Consistent with this hypothesis, we find that inactivating mutations in the RSK1 kinase domains disrupted the mitogen-regulated dissociation of ERK1/2 in vivo. Analysis of different RSK isoforms revealed that RSK1 and RSK2 readily dissociate from ERK1/2 following mitogen stimulation but that RSK3 remains associated with active ERK1/2. RSK activity assays revealed that RSK3 also remains active longer than RSK1 and RSK2, suggesting that prolonged ERK association increased the duration of RSK3 activation. These results provide new evidence for the regulated nature of ERK docking interactions and reveal important differences among the closely related RSK family members. Phosphorylation of p90 ribosomal S6 kinase (RSK) regulates extracellular signal-regulated kinase docking and RSK activity. Philippe Roux Stephanie Richards John Blenis Mol Cell Biol, Vol. 23, No. 14. (Jul 2003), pp. 4796-4804. 2007-12-04T03:22:10-00:00 2003 Mol Cell Biol 23 14 4796 4804 90-kda amino-acid article-predikin binding cell cultured data epidermal extracellular factors growth homology human isoenzymes kinase matrix mitogen-activated mitogens molecular mutation phosphorylation protein ribosomal s6 sequence serine signal sites structure tertiary transduction