Abstract: The present invention provides a synthetic gene control region which comprises a gene regulatory sequence comprising a binding site for a gene regulatory protein of a yeast strain, and a promoter from filamentous fungal strain located downstream of the gene regulatory sequence; wherein the promoter can be recognized by the general transcription factors and RNA polymerase of the yeast strain; wherein the gene regulatory sequence is capable of regulating transcription initiated by the filamentous fungal promoter in the yeast strain.

Abstract: The present invention provides a synthetic gene control region which comprises a gene regulatory sequence comprising a binding site for a gene regulatory protein of a yeast strain, and a promoter from filamentous fungal strain located downstream of the gene regulatory sequence; wherein the promoter can be recognized by the general transcription factors and RNA polymerase of the yeast strain; wherein the gene regulatory sequence is capable of regulating transcription initiated by the filamentous fungal promoter in the yeast strain.

Abstract: A method for determining a matrix of expression levels corresponding to a set of biological targets (e.g., genes or gene fragments) and a set of biological samples, including obtaining a matrix of signal values corresponding to the set of biological targets; computing a vector of expression levels for a sample in the set of biological samples using the matrix of signal values; storing the vector of computed expression levels in a storage matrix; repeating the computing and storing steps for each sample in the set of biological samples; and outputting the storage matrix as the matrix of expression levels. The method, based on a linear programming formulation of the problem, works for both “promiscuous” probe array data, in which there may be multiple targets indicated by a single probe, and the “polygamous” case, in which there are multiple probes for a single target. The preferred method can also process data obtained from multiple SAGE analyses using multiple markers.

Abstract: A method for determining a matrix of expression levels corresponding to a set of biological targets (e.g., genes or gene fragments) and a set of biological samples, including obtaining a matrix of signal values corresponding to the set of biological targets; computing a vector of expression levels for a sample in the set of biological samples using the matrix of signal values; storing the vector of computed expression levels in a storage matrix; repeating the computing and storing steps for each sample in the set of biological samples; and outputting the storage matrix as the matrix of expression levels. The method, based on a linear programming formulation of the problem, works for both “promiscuous” probe array data, in which there may be multiple targets indicated by a single probe, and the “polygamous” case, in which there are multiple probes for a single target. The preferred method can also process data obtained from multiple SAGE analyses using multiple markers.