Method and system for analyzing biological response signal data

A method for processing biological signal profile data for storage in a central biological database server and for retrieval therefrom by a user computer connected to the central database server across a computer network, comprising the steps of:

• storing a plurality of biological signal profiles in said central database server;
• computing a correlation metric between at least one of said plurality of biological signal profiles and other of said plurality of biological signal profiles in said central database server;
• storing said correlation metrics in said central database server in conjunction with said expression array experiments;
• at said user computer, at a time subsequent to said step of storing said correlation metrics, selecting a query profile and a target set of biological response profiles from among said plurality of biological response profiles in said central database server;
• receiving correlation criteria and a correlation execution command from a user at said user computer;
• querying said central database server to identify biological response profiles between said source set and said target set having correlation metrics that satisfy said correlation criteria;
• transmitting information related to said identified biological response profiles and related correlation metrics from said cental biological database server to said user computer;
• and
• displaying information derived from said biological response profiles and related correlation metrics at said user computer;
• whereby real time computation of said correlation metrics is not required at said user computer after said correlation execution command, thereby enhancing speed of biological correlation analysis at said user computer.

A computer program product for directing a user computer to perform dynamic menu generation for receiving a required biological data field selection from a user, the user computer connected to a central database server across a computer network, said computer program comprising:

• computer code for querying said central database server upon instantiation of said computer program product on said user computer, said query being adapted to request dynamic menu information from said central database server, said dynamic menu information defining biological data field items, subcategory items, and submenuing relationships among said biological data field items and subcategory items;
• computer code for displaying a first menu on a user display, said first menu comprising at least a portion of said biological data field items and subcategory items;
• computer code for receiving a first menu selection from the user;
• computer code for determining whether said first menu selection is a biological data field or a subcategory item;
• computer code for identifying said first menu selection as the required biological data field selection if said first menu selection is a biological data field;
• and
• computer code for identifying submenu information contained in said dynamic menu information if said first menu selection is a subcategory item, and for displaying said submenu information on a second menu near said first menu on said user display;
• whereby said user computer is not required to store dynamic menu information, said central database server being capable of storing substantially all required dynamic menu information, allowing for enhanced flexibility and customization capability of biological menu systems on said user computer.

A method for analyzing expression array data using a computer, the expression array data being derived from machine readable outputs of perturbation experiments performed on a plurality of biological samples, comprising the steps of:

• generating a coregulation tree using said expression array data;
• displaying said coregulation tree in a hyperbolic display format;
• manipulating the display of the coregulation tree to display a first gene or gene product located on a branch thereof, said first gene or gene product having a known function;
• locating a second gene or gene product on said coregulation tree on the same branch as said first gene or gene product;
• and
• assigning a function to said second gene or gene product using information related to said known function of said first gene or gene product and information related to a positional relationship or distance metric between said second gene or gene product and said first gene or gene product on said branch of said coregulation tree.

A method for analyzing expression array data using a computer, the expression array data being derived from machine readable outputs of perturbation experiments performed on a plurality of biological samples, comprising the steps of:

• generating an experiment profile cluster tree using said expression array data;
• displaying said experiment profile cluster tree in a hyperbolic display format;
• manipulating the display of the experiment profile cluster tree to display a first experiment located on a branch thereof, said first experiment corresponding to a known function of a perturbation assayed therein;
• locating a second experiment on said experiment profile cluster tree on the same branch as said first experiment;
• and
• assigning a function to a biological perturbation assayed in said second experiment using information related to said known function of said perturbation assayed in said first experiment and information related to a positional relationship or distance metric between sail second experiment and said first experiment on said branch of said experiment profile cluster tree.