Boston University Bioinformatics IGERT
Student Research Figures
Below are figures from recent student publications.
Tim Reddy 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).
Steve Parker (this paper was done with Jay Greenbaum, a former student) 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.
Michael Driscoll 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.
Joe Mellor 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.
Joe Mellor 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