Table 2.

Descriptive statistics for RNG/MRC, Affymetrix, Agilent and Illumina probe collections

	Human		Mouse
	Probes	Transcripts	Probes	Transcripts
Number of distinct RNG/MRC sequences	148 993	29 894	121 703	26 058
Number of distinct gene symbols	—	21 043	—	22 740
Total number of RNG/MRC probes	25 342	29 894	24 109	25 002
Number of RNG/MRC probes with x_hyb = 0	17 457	—	16 767	—
Number of RNG/MRC probes with x_hyb = 1,x	5921	—	5563	—
Number of RNG/MRC probes with x_hyb > 1,y	1964	—	1779	—
Average EST_NUMBER per RNG/MRC probe	53	—	39	—
Average DIST_TO_3′score per RNG/MRC probe	692	—	488	—
Affymetrix U133Plus2 / MG-U74	108 371a	27 588b	89 502a	20 624b
Agilent whole genome	40 990	25 627b	20 865	18 087b
Illumina human / MEEBO	22 548	21 271b	36 362	22 463b

Oligonucleotides with X_HYBRID equal to 0 or to 1,x are considered ‘BLAST-specific’ probes; oligonucleotides with a X_HYBRID equal to x,y (x > 1) can possibly cross-hybridize with other transcripts. They were selected only when no better probe was available for a given transcript. For Affymetrix, comparison was performed for the first and last 25mer probes of each perfect-match Affymetrix probe sets (a probe set is specific to a gene and is composed of an average of ten 25mer probes). A total of 90% of the transcripts have a majority of their associated oligonucleotides characterized by a X_HYBRID score below 2. Less than 5% of the transcripts are only associated with oligonucleotides characterized by a X_HYBRID score above 2.

^aOnly the first and last probes from each Affymetrix probe set were used for analysis.

^bNumber of transcripts matched by probes from the RNG/MRC transcript selection set.