Methods for monitoring multiple gene expression

1. A non-transitory computer readable medium having recorded thereon

an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof, selected from the group consisting of SEQ ID NOs. 1-1188 for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells;

a computer readable program code for performing the step of examining the array under conditions wherein the relative expression of the genes in the first and one or more second filamentous fungal cells is determined by the observed detection signal of each spot in the array in which (i) the Trichoderma reesei ESTs or SSH clones, or a combination thereof, in the array that hybridize to the nucleic acids obtained from either the first or the one or more second filamentous fungal cells produce a distinct first detection signal or one or more second detection signals, respectively, and (ii) the Trichoderma reesei ESTs or SSH clones, or a combination thereof, in the array that hybridize to the nucleic acids obtained from both the first and one or more second filamentous fungal cells produce a distinct combined detection signal; wherein the hybridization conditions are selected from the group consisting of very low, low, low-medium, medium, medium-high, high, and very high stringency condition.

2. The computer readable medium of claim 1 , wherein the magnetic storage medium is selected from the group consisting of a floppy disk, a hard disk, and a magnetic tape.

3. A computer-based system for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells comprising:

the non-transitory computer readable medium of claim 1 ; and

a processor for performing the step of examining data obtained from the array under conditions wherein the relative expression of the genes in the first and one or more second filamentous fungal cells is determined by the observed detection signal of each spot in the array in which (i) the Trichoderma reesei ESTs or SSH clones, or a combination thereof, in the array that hybridize to the nucleic acids obtained from either the first or the one or more second filamentous fungal cells produce a distinct first detection signal or one or more second detection signals, respectively, and (ii) the Trichoderma reesei ESTs or SSH clones, or a combination thereof, in the array that hybridize to the nucleic acids obtained from both the first and one or more second filamentous fungal cells produce a distinct combined detection signal; wherein the hybridization conditions are selected from the group consisting of very low, low, low-medium, medium, medium-high, high, and very high stringency condition.

4. The computer-based system of claim 3 , wherein the magnetic storage medium is selected from the group consisting of a floppy disk, a hard disk, and a magnetic tape.

5. The computer readable medium of claim 1 , wherein the optical storage medium is selected from the group consisting of a CD-ROM and a DVD.

6. The computer readable medium of claim 1 , wherein the electrical storage medium is selected from the group consisting of RAM and ROM.

7. The computer-based system of claim 3 , wherein the optical storage medium is selected from the group consisting of a CD-ROM and a DVD.

8. The computer-based system of claim 3 , wherein the electrical storage medium is selected from the group consisting of RAM and ROM.