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    Feed Forward Loop

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    Radu Siniavschi
    The document describes a feed-forward loop (FFL), which is a network motif consisting of two input transcription factors that each regulate a third gene. FFLs can be coherent or incoherent depending on whether the transcription factors activate or repress their shared target. The document then discusses the structure of FFLs using E. coli as an example, and how coherent and incoherent FFLs function differently to filter signals, respond to stimuli, and shut down responses. It proposes a database to integrate information on FFLs from different organisms.

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    Feed Forward Loop

    Uploaded by

    Radu Siniavschi
    73 views19 pages
    The document describes a feed-forward loop (FFL), which is a network motif consisting of two input transcription factors that each regulate a third gene. FFLs can be coherent or incoherent depending on whether the transcription factors activate or repress their shared target. The document then discusses the structure of FFLs using E. coli as an example, and how coherent and incoherent FFLs function differently to filter signals, respond to stimuli, and shut down responses. It proposes a database to integrate information on FFLs from different organisms.

    Original Description:

    Resume and comments on using Feed Forward Loop to discover motifs

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    The document describes a feed-forward loop (FFL), which is a network motif consisting of two input transcription factors that each regulate a third gene. FFLs can be coherent or incoherent depending on whether the transcription factors activate or repress their shared target. The document then discusses the structure of FFLs using E. coli as an example, and how coherent and incoherent FFLs function differently to filter signals, respond to stimuli, and shut down responses. It proposes a database to integrate information on FFLs from different organisms.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    73 views19 pages

    Feed Forward Loop

    Uploaded by

    Radu Siniavschi
    The document describes a feed-forward loop (FFL), which is a network motif consisting of two input transcription factors that each regulate a third gene. FFLs can be coherent or incoherent depending on whether the transcription factors activate or repress their shared target. The document then discusses the structure of FFLs using E. coli as an example, and how coherent and incoherent FFLs function differently to filter signals, respond to stimuli, and shut down responses. It proposes a database to integrate information on FFLs from different organisms.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 19

    BACA THEODOR-STEFAN and SINIAVSCHI RADU MASTER ITEMS 2012

    FEED-FORWARD LOOP CENTRAL DATABASE

    Based on the article: STRUCTURE AND FUNCTION OF THE FEED-FORWARD LOOP NETWORK MOTIF by S. Mangan and U. Alon

    What is a FEED-FORWARD LOOP?


    Feed-forward loop (FFL) is a motif, consisting in a three-gene pattern composed of two input transcription factors. Each of the three interactions in the FFL can be either activating or repressing (coherent or incoherent).
    Simple regulation of Z by X and Y.

    Transcription factor X regulates transcription factor Y, and both jointly regulate Z. Sx and Sy are the inducers of X and Y, respectively. The action of X and Y is integrated at the Z promoter with a cisregulatory input function , such as AND or OR logic.

    FFL- Structure
    E. coli example:

    COHERENT and INCOHERENT FFL type

    Decide from fluctuating signal Filter out pulses Respond to persistent stimulations Rapidly shut down

    Easly reverse Initially reacts strongly Later comes back to intermediate levels

    FFL- Structure
    Logic function
    AND OR

    logic

    logic

    X and Y respond to

    external stimuli

    Coherent Type-1 FFL AND logic


    Sx appear, X rapidly changes to X*

    X* binds to gene Z, but cannot activate it X* binds to gene Y, and begins to transcript it Z begins to be expressed after Ton time, when Y* crosses the activation threshold Kyz

    Incoherent Type-1 FFL

    MATERIALS AND METHODS


    Equations for Gene Regulation Reactions

    MATERIALS AND METHODS


    Parameters for Functional FFLs

    RESULTS

    RESULTS

    RESULTS

    RESULTS

    The FFL Database


    An user-friendly web app that integrates feed forward loops so scientists and other enthusiasts could use the results for educational and scientifical purposes.

    The FFL Database


    An user-friendly web app that integrates feed forward loops so scientists and other enthusiasts could use the results for educational and scientifical purposes.

    The actual FFL Database

    Methods of FFL Database

    Search where we can get information about the regulatory networks Get from the information about the regulation by Transcription Factors. Construct an algorithm to extract the FFL motives different organisms

    regulatory networks.
    Make a hierarchical clasiffication of FFLs elements. Make a clasiffication acording to the origin of the signal that TFs sense. Search for differences betwen the data on each position of the FFLs

    making statistical tests to validate significance.

    CONCLUSIONS
    Incoherent FFLs sign-sensitive accelerators. Coherent FFLs sign-sensitive delays. Some FFL occur more often than the others. Observe how TFs that detect different-origin signals compose Observe the dinamics on the TRN looking for the formation of specific

    topological structure, FFL


    Search for significative differences on the data by statistical tests on

    each position of the FFLs.

    Thank you for your attention!

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