The Fgenesh exon predictions were made by the authors of Ref. 34 (Hild et al.,Genome Biol. 5, R3 (2003)). The prediction are listed in HDC_exons.gff.
To obtain the exons belonging to novel predicted genes, we subtracted all the basepairs annotated as exons of release 3.1. We subsequently merged the genes into clusters and obtain the file HDC_exons_gM_c100_MINUS_GADFLY.gffgc100.

We downloaded from the URL http://genomebiology.com/content/supplementary/gb-2003-5-1-r3-s3.pdf, the micro-array data of Ref. 34. This pdf file is converted into a textfile, called Hildetal_exp.txt.
We selected the assayed novel gene predictions that were expressed according to the M-CHIPs analysis (see  Methods section "filtering and data acquisition" of Ref. 34). The expressed genes that did not overlap with pseudogenes, repeats and transposons are listed in Hildetal_exp_expr_MINUSGADFLY.txt.
Next we obtained the exons of expressed novel predicted genes by taking the overlap of expressed genes in the latter file and those for which we have exons (file HDC_exons_gM_c100_MINUS_GADFLY.gffgc100).

We found that 415 NEPs are located inside exons of expressed novel predicted genes. Of these, 260(62.7%) were significantly expressed according to PEAB. The 415 NEPs is significantly (P=4.16E-19) enriched for expressed NEPs compared to 41% of NEPs that were expressed above noise.



SUMMARY OF FILES:

HDC_exons.gff  - see above.

HDC_exons_gM_c100_MINUS_GADFLY.gffgc100 - see above.

Hildetal_exp.txt - see above.

Hildetal_exp_expr_MINUSGADFLY.txt -see above.

Overlap_ExpressedNovelFgeneshExons_with_NEPs.txt:
List of 415 NEPs that belong to exons of novel predicted expressed genes. 
The ids of probes and exons and their locations are listed.

Overlap_ExpressedNovelFgeneshExons_with_ExpressedNEPs.txt:
260 expressed NEPs that confirm the novel predicted genes that were expressed according to MCHIP analysis. 

Reported in the main text of the article were the numbers of (expressed) NEPs that were located inside assayed exons.
For the overlap of assayed exons with all NEPs we obtained the file
  Overlap_AssayedNovelFgeneshExons_with_NEPs.txt (777 probes). 
In case of expressed NEPs, the results are listed in file
  Overlap_AssayedNovelFgeneshExons_with_ExpressedNEPs.txt (477 probes).