A method for creating a transcriptome-wide expression profile that involves measuring the expression of only a subset of the total number of transcripts, comprising: a) providing; i) a plurality of sample transcripts derived from a biological sample; ii) a plurality of centroid transcripts comprising at least a portion of said sample transcripts, said remaining sample transcripts being non-centroid transcripts wherein a centroid transcript is a transcript that is within the center portion, or is representative of a transcript cluster, wherein a non-centroid transcript is a transcript in a transcript cluster that is not a centroid transcript, and wherein transcript clusters are identified by a computational analysis of the transcripts derived from a transcriptome; b) measuring the expression level of said plurality of centroid transcripts; c) inferring the expression levels of said non-centroid transcripts from said centroid transcript expression levels without measuring the expression level of the non-centroid transcripts, wherein the expression level of a non-centroid transcript is predicted by the expression levels of centroid transcripts using a dependency matrix that relates the expression levels of a plurality of cluster centroid landmark transcripts to the expression levels of non-centroid transcripts; and d) combining the results of step b and step c, thereby creating a transcriptome-wide expression profile. a) providing; i) a plurality of sample transcripts derived from a biological sample; ii) a plurality of centroid transcripts comprising at least a portion of said sample transcripts, said remaining sample transcripts being non-centroid transcripts wherein a centroid transcript is a transcript that is within the center portion, or is representative of a transcript cluster, wherein a non-centroid transcript is a transcript in a transcript cluster that is not a centroid transcript, and wherein transcript clusters are identified by a computational analysis of the transcripts derived from a transcriptome; i) a plurality of sample transcripts derived from a biological sample; ii) a plurality of centroid transcripts comprising at least a portion of said sample transcripts, said remaining sample transcripts being non-centroid transcripts wherein a centroid transcript is a transcript that is within the center portion, or is representative of a transcript cluster, wherein a non-centroid transcript is a transcript in a transcript cluster that is not a centroid transcript, and wherein transcript clusters are identified by a computational analysis of the transcripts derived from a transcriptome; b) measuring the expression level of said plurality of centroid transcripts; c) inferring the expression levels of said non-centroid transcripts from said centroid transcript expression levels without measuring the expression level of the non-centroid transcripts, wherein the expression level of a non-centroid transcript is predicted by the expression levels of centroid transcripts using a dependency matrix that relates the expression levels of a plurality of cluster centroid landmark transcripts to the expression levels of non-centroid transcripts; and d) combining the results of step b and step c, thereby creating a transcriptome-wide expression profile.