Statistical Summary of CAMDA '04 Contest Datasets

"Complete" Dataset
7091	Oligos in "Complete" dataset
-216	Oligo_ID is "empty"
6875	Unique Oligo_IDs
-1265	"NULL" Gene ID (No "annotations" are present but 690 had some comments) [Note: "NULL" string here is not the same as "null" in database terminology]
-2	GeneID was missing (E9299_3 and N1) ["null" in database terminology]
5608	Oligos with associated GeneIDs. [Annotation field missing for Oligo_IDs: F23846_3, oPFF72466] 4314 unique GeneIDs. 35 genes have 5 or more oligos; Gene MAL6P1.147 represented by 15 oligos.
"Quality Control Set"
5071	Oligos in "Complete" set of 6875 unique oligos
+9	"New" oligos not in "Complete" set: opfrr0006, ptrgln, ptrgly, ptrgly2, ptrphe, ptrpro, ptrthr, ptrtrp, snr1
5080	Unique oligos in "Quality Control Set" Bozdech: "Fourier analysis was performed on each profile in the quality-controlled set (5081 oligonucleotides)."
-555	"NULL" Gene ID (but 87 had some comments)
4525	Oligos with associated GeneIDs. [Annotation field missing for 30 Oligos] 3533 unique Gene IDs. 3529 unique Gene IDs are in the list of unique Gene IDs from the "Complete" set. The four new Gene IDs are: ITS2, P, Plastid Genome, snRNA? 24 genes have 5 or more oligos; Gene "Plastid Genome" represented by 27 oligos; Gene MAL6P1.147 represented by 15 oligos; Gene PFI1475w represented by 10 oligos.
"Overview" Dataset
3711	Oligos in "Complete" set of 6875 unique oligos
+8	"New" oligos not in "Complete" set and introduced in the QC set: ptrgln, ptrgly, ptrgly2, ptrphe, ptrpro, ptrthr, ptrtrp, snr1
3719	Unique oligos in "Overview" dataset . All "Overview" oligos are in the QC dataset.
-335	"NULL" Gene ID (but 56 had some comments)
3384	Oligos with associated GeneIDs. 2687 unique Gene IDs Gene "P" in the QC Dataset was renamed to Gene "PF14_0338" in the Overview set. The annotation information for these three genes changed slightly between the QC dataset and the Overview dataset: PFE0040c, PF11_0358, PF14_0451. Note: Bozdech reports in the P. falciparum Transcriptome Overview: "The overview set represents 2714 unique ORFs (3395 oligonucleotides). An additional 324 oligonucleotides represent ORFs that are not currently part of the manually annotated collection." The caption to Figure 2 shows "transcriptional profiles for 2712 genes".