Welcome to the University of Texas Bioinformatics, Proteomics, and Functional Genomics server


Web Services
  • YEASTNET



    YeastNet v. 2 is a probabilistic functional gene network of yeast genes constructed using a modified Bayesian integration of diverse data types, with each data type weighted according to how well it links genes that are known to share functions.

  • PROTEIN LINK EXPLORER (PLEX)



    PLEX is a web based tool allowing you to create a phylogenetic profile for any given protein, and then compare the profile with profiles of more than 300,000 proteins in our database.

    Plex references:
    Date and Marcotte. The Protein Link Explorer (manuscript in preparation).

  • LARGE GRAPH LAYOUT (LGL)



    LGL is a compendium of applications for making the visualization of large networks and trees tractable. LGL was specifically motivated by the need to make the visualization and exploration of large biological networks more accessible. Essentially the network is a graph, which is the data that you define, and LGL is responsible for showing it to you.

    LGL references:
    Adai, Date, McDonald and Marcotte. Large Graph Layout (J. Mol. Biol., in press).

  • ROSETTA STONE PROTEIN LINKS



    Find Rosetta stone links for genes - coming soon!!

    Rosetta stone links' references:
    Date and Marcotte. The Protein Link Explorer (manuscript in preparation).

  • GENE NEIGHBORS



    Find gene pairs and genes arranged in operon-like groups based on an user-specified distance. Parameters like strand exclusion and overlap allowed can be set, giving the user ability to investigate a genome in fair detail.

    Gene Neighbors' references:
    Date and Marcotte. The Protein Link Explorer (manuscript in preparation).

  • M.tuberculosis protein network



    Approximately 2,906 unique functional linkages have been established between 2,772 (71%) of the 3,927 proteins of Mycobacterium tuberculosis (TB) by comparative genomics methods. Functional links are predicted between TB proteins that are coinherited (as measured with phylogenetic profiles), that are found as fusion genes in other genomes (using the Rosetta Stone method), and that are found as adjacent proteins in operons (using the method of Salgado et al., PNAS 97:6652-7 (2000). Annotions for the TB genes are taken from the Sanger Center.


  • MATRIX - Co-evolution Simulation



    A server for exploring the prediction of protein interactions by matching phylogenetic trees of interacting proteins, as described in the J. Mol. Biol. paper "Exploiting the co-evolution of interacting proteins to discover interaction specificity". More information can be obtained from JMB 2003; 327(1):273-284.here

  • the MoBIoS Project - Molecular Biological Information System



    The goal of the project is to invent a new generation database management system for molecular biological data, based on metric space indexing techniques and a database query language embodying the semantics of genomic and proteomic data.

Databases
  • LONGHORN ARRAY DATABASE (LAD)



    The Longhorn Array Database (LAD) is an open source, MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a freely available implementation of the Stanford Microarray Database (SMD).

    LAD references:
    Killion and Iyer. BMC Bioinformatics 2003 4:32.

  • OPEN PROTEOMICS DATABASE (OPD)



    The Open Proteomics Database (OPD) is a public database for storing and disseminating mass spectrometry based proteomics data. The database currently contains ~400,000 spectra representing experiments from 4 different organisms.

    OPD references:
    Prince, Carlson, Wang, Lu and Marcotte. Nature Biotechnology 2004 22:471-2.

Supplementary information for manuscripts

Supplementary information: Date and Marcotte, Nature Biotechnology 21(9):1055-62 (2003)
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages

Supplementary information: Lu, Nakorchevskiy and Marcotte, Proc. Natl. Acad. Sci., USA, 100(18), 10370-5 (2003).
Expression deconvolution: A reinterpretation of DNA microarray data reveals dynamic changes in cell populations

Supplementary information: Dhillon, Marcotte and Roshan, Bioinformatics, 19(13):1612-9 (2003)
Diametrical clustering for identifying anti-correlated gene clusters

Supplementary information: Adai, Date, McDonald and Marcotte, J. Mol. Biol.(in press, 2004)
LGL: Creating a map of protein function with an algorithm for visualizing very large biological networks

Supplementary information: Prince and Marcotte, Anal. Chem., 78(17): 6140-52 (2006)
Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpolated Warping

Questions/Comments: Email svdate AT ccwf dot cc dot utexas dot edu
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