Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology

BMC Genomics

Table 1 Number of features analyzed in comparisons for all 6 platforms/protocols

Platforms /Protocols	# Features at probe(set) & exon level	# Non-control features at probe(set) & exon level	# Features at gene & transcript cluster level	# Genes in RefSeq & Ensembl gene database	# Detected genes & transcript clusters *	# Genes & transcript clusters for 15442 common RefSeq genes	# Probe(set)s & exons for transcript pattern restricted 7034 RefSeq genes	# Probe(set)s & exons for transcript pattern not restricted 7034 RefSeq genes
AGLN	43,376	41,000	29,066	24,961	22,056	15,442	8,668	11,453
Gene1.0	257,430	253,002	28,869	20,796	28,105	16,516	11,449	84,196
HTA2.0	914,585	573,909	67,526	25,195	67,309	16,400	14,908	138,484
ILMN	47,306	47,214	34,589	31,320	23,377	15,442	8,539	11,414
ClonTech	1,298,791	1,298,791	62,893	49,085	43,266	15,594	16,470	334,318
RiboZero	1,298,791	1,298,791	62,893	52,865	48,378	15,594	16,470	334,318

Notes:
1. AGLN: 41,000 probes represent 29,066 genes by GeneSymbol & SystematicName; 29,066 “genes” are composed of 24,961 entries with symbols and 4,105 with Agilent probe_ids only
2. Gene1.0: 253,002 probesets represent 28,869 genes by Affymetrix “transcript_cluster_id” (TC); 28,869 TCs are composed of 20,796 genes with symbols and 6,209 without symbols (NetAffx na33.2)
3. HTA2.0: 573,909 probesets represent 67,526 genes by Affymetrix “transcript_cluster_id” (TC); 67,526 TCs are composed of 25,195 genes with symbols and 40,696 without symbols (NetAffx na33)
4. ILMN: 47,214 probese represent 34,589 Illumina named “genes”, of which 31,320 have official gene symbols and 3,269 labeled with Unigene_ids (Hs.xxxxxx)
5. ClonTech: 1,298,791 exons represent 62,893 ensembl genes (ENSGs) in R72 database; 62,893 down to 49,085 ENSGs with at least 1 read in any of 5 samples
6. RiboZero: 1,298,791 exons represent 62,893 ensembl genes (ENSGs) in R72 database; 62,893 down to 52,865 ENSGs with at least 1 read in any of 5 samples
*A “detected” call for AGLN at gene level and for Gene1.0 and HTA2.0 at transcript cluster level was made if any probe(set) was “detected” in any sample by p < 0.05 (AGLN) or p < 0.01 (Gene1.0 & HTA2.0); and for RNA-seq data the detection calls were made if any samples had a cpm >0.25. ILMN data have “detected” calls by p < 0.05 at both probe and gene levels

ISSN: 1471-2164