Lab: Charles DeLisi
Citation: The paper is at the end of preparation, and will be submitted for review very soon.
Caption: Architecture of functional- and nonfunctional-TATA promoters. Yeast TATA-containing promoters were divided into functional-TATA andnonfunctional-TATA based on microarray experiments performed in (Chitikila et al, 2000). Value of various promoter features were averaged using a sliding window across functional-TATA (red), nonfunctional-TATA (blue), and genomic (black) promoters. The vertical gray band indicates the peak of TATA-box enrichment in the promoters.The FTPs are significantly enriched in G/C 4mers (top row), have a preference for nucleosomes (Ioshikhes et al, 2006) near the TATA box (middle row), and avoid weak TBP binding sites in the extended promoter (bottom row). The average length of the FTPs (red square) is117bp (21%) longer than the NTPs (blue square); and is 130bp (24%) longer genomic promoters (black square). Horizontal bars indicate a significant (p<1e-5) difference between FTPs and genome average for each feature. Significance was calculated using a normal approximation to a binomial distribution for GC 4mers and weak TATA consensus sequences (35bp window), and a one sided U-test for nucleosome positions (20bp window).
Lab: Tom Tullius
Citation: Greenbaum JA, Parker SC, Tullius TD. Detection of DNA structural motifs in functional genomic elements. Genome Res. 2007 Jun;17(6):940-6.
Caption: This figure shows DNA structural characteristics, measured by hydroxyl radical cleavage, of motifs that were discovered in DNase I hypersensitive sites in the human genome. These sites are highly similar in structure but not in sequence.
Lab: Tim Gardner
Citation: ME Driscoll, MF Romine, FS Juhn, MH Serres, LA McCue, AS Beliaev, JK Fredrickson, TS Gardner (2007) Identification of Diverse Carbon Source Utilization Pathways in Shewanella oneidensis MR-1 via Expression Profiling. Genome Informatics, accepted.
Caption: Expression of enzymes involved in pathways related to inosine metabolism in the metal-reducing microbe Shewanella oneidensis MR-1. Red and blue colors indicate up and down-regulation, respectively, during growth with inosine; circle circumference represents absolute levels of expression. (A) A liberated ribose moiety from inosine is thought to be converted to fructose-6-phosphate by the non-oxidative branch of the pentose phosphate cycle, and fed into the Entner-Doudoroff pathway. (B) Repression of genes involved in the first steps of purine synthesis, for which inosine-5-phosphate is a key intermediate; for brevity, not all metabolites are shown. (C) Expression of three key gene neighborhoods in their genomic contexts.
Lab: Biomolecular Systems Laboratory
Citation: Hu, Z., Mellor, J., Wu, J. and DeLisi, C. (2005) VisANT: data-integrating visual framework for biological networks and modules, Nucl. Acids Res. 2005 33: W352-W357.
Caption: This figure shows a functional view of regulatory interactions in Saccharomyces cerevisiae, and how different levels of function and interactions can be integrated within VisANT. Each outer (pink) group of genes have the same Gene Ontology (GO) annotation at a given level of specificity, with all GO processes of fixed depth represented. Inner green objects are transcription factors, Fhl1p, Ste12p, and Mcm1p (from left to right), and their published regulatory interactions with other genes throughout the yeast genome (protein-DNA binding determined by ChIP chip, Lee, et al, Science 2002). The key feature of this view is how transcription factors combine to selectively control particular groups of biological processes. The central shaded region shows the pheromone response (MAPK) pathway in yeast (from the KEGG database) with its downstream regulating proteins Ste12p and Mcm1p. The smaller dark box in the upper left represents the entire pathway of cell-cycle control in yeast, only here the pathway has been collapsed to hide its internal structure and connections. Instead, connections here show regulatory interactions involving individual protein components of the pathway (in yellow) or shared-gene components between the cell cycle and GO functional categories (in blue). This shows how genes involved in cell-cycle control are connected to other genes and processes throughout the cell by both physical and functional interactions.
Lab: Biomolecular Systems Laboratory
Citation: Hu, Z., et al., (2007) Towards zoomable multidimensional maps of the cell. Nat Biotechnol, 25(5): p. 547-54.
Caption: A metagraph of the network of protein complexes discovered through tandem affinity mass spectrometry tagging by Gavin et al. and grouped and colored to indicate subsequent functional assignments. The gray edges connect complexes that share protein components. The components of each complex are included in the model and are visible when the metanode representing the complex is expanded. Exepmplar complexes from each function are expanded to show individual proteins and overlaps in their protein complex membership