Methods and systems for visualizing gene expression data

A non-transitory computer-readable storage medium tangibly encoded with computer readable instructions, that when executed by a processor associated with a computing device, performs a method for visualizing and analyzing gene expression data, the method comprising:

• receiving from a database, a digital file comprising one or more sets of long range gene expression data for one or more patients;
• loading said long range gene expression data into an analytical tool comprising a user interface and data storage, wherein said user interface is configured to receive commands from and to provide feedback to an operator;
• in response to receiving from the operator of said user interface, instructions defining the size of at least one window for evaluating said long range gene expression data, wherein said window size is measured by sequence size in kb, inputting said defined window size into said analytical tool;
• converting the long range gene expression data for at least one patient into a series of concatenated windows that are the size of said defined windows;
• identifying, by said processor, each gene that is contained within each of said windows;
• generating a sample-specific gene abundance score for each of said genes using transcript abundance estimation software stored in said processor;
• calculating, by said processor, an average gene abundance score for all of the genes identified in each of said windows;
• and
• presenting the average gene abundance scores for at least some of the windows in a two-dimensional array, wherein one axis of the array organizes the windows by patient and the other axis of the array organizes the windows by gene sequence.

A system for visualizing and analyzing gene expression profile data, comprising;

• one or more non-transitory computer-readable storage devices tangibly encoded with computer readable instructions, that when executed by a processor associated with a computing device, performs a method comprising:
• receiving from a database, a digital file comprising one or more sets of long range gene expression data for one or more patients;
• loading said long range gene expression data into an analytical tool comprising a user interface and data storage, wherein said user interface is configured to receive commands from and to provide feedback to an operator;
• in response to receiving from the operator of said user interface, instructions defining the size of at least one window for evaluating said long range gene expression data, wherein said window size is measured by sequence size in kb, inputting said defined window size into said analytical tool;
• converting the long range gene expression data for at least one patient into a series of concatenated windows that are the size of said defined windows;
• identifying, by said processor, each gene that is contained within each of said windows;
• generating a sample-specific gene abundance score for each of said genes using transcript abundance estimation software stored in said processor;
• calculating, by said processor, an average gene abundance score for all of the genes identified in each of said windows;
• and
• presenting the average gene abundance scores for at least some of the windows in a two-dimensional array, wherein one axis of the array organizes the windows by patient and the other axis of the array organizes the windows by gene sequence.