Table 3.

Classification of 17-Base Genomic and Expressed Signatures

			Secondary class
Class	Position	Arabidopsis genome^a	3	6	# with hits = 1	% with hits = 1^b	Grouped by gene^c	Mean # per gene	# in MPSS libraries^d	MPSS data, grouped by gene^d
1	Within exon, same strand	203,174	204	149	168,024	82.7	28,134	7.22	29,352	16,312
2	Within 500 bp potential 3′UTR	44,536	7,047	733	37,831	84.9	21,735	2.05	6,844	5,862
3	Antisense to exon	197,083	—	—	163,052	82.7	27,813	7.09	16,897	9,474
4	Unannotated	288,142	—	—	223,609	77.6	—	—	5,622	—
5	Within intron, sense strand	60,430	153	107	53,639	88.8	17,003	3.55	1,476	1,317
6	Within intron, antisense strand	57,847	—	—	51,354	88.8	16,715	3.46	685	650
7	Spans an exon/intron splice site	6,807	—	—	5,652	83.0	5,369	1.27	955	920
	Total	858,019	7,404	989	703,161	82.0	28,912		61,831	19,820
0	Non genomic match		—	—			—	—	19,970
1/2/5/7	Normal coding gene	314,947	—	—			28,911		38,627	19,088

↵a Number of signatures occurring at distinct positions in TIGR annotation version 3.0.
↵b Calculated as the number of signatures in each class with hits = 1 divided by the total number of signatures in that class.
↵c This value is the union of the set of gene identifiers matched by all genomic signatures in each class.
↵d From 14 libraries, considering only “significant” and “reliable” expressed signatures for which hits = 1, and excluding 37,192 “nonsignificant” hits to the genome. Calculated as the union of the set of all libraries.

The Use of MPSS for Whole-Genome Transcriptional Analysis in Arabidopsis