Column definition for tars.txt files
----------------------------------------

chr: Arabidopsis chromosome on which TAR is located

start: Start position of the TAR (first nucleotide of the most 5'
probe inclusive to the TAR)

stop: End position of the TAR (last nucleotide of the most 3' probe
inclusive to the TAR)

num_probes: Number of tiling probes inclusive to the TAR

level: Predicted discrete expression level of this TAR (between 1 and
10)

repeats: Fraction of repetitive probes inclusive to this TAR (repeat
annotation is based on degenerate 25-mer repeats in the A. thaliana
genome, see Clark et al, Science, 2007 for details)

high_confidence: TARs with at least 4 probes, expression level 6-10
and repetitive proportion less than 0.25 are called 'high-confidence'
TARs.

unannotated: 0 if there is an overlap of at least 25 nt to one or
more exons of an (or several) annotated gene(s)

novel: 0 if there is an overlap of at least 25 nt to an EST or cDNA,
else 1 (ESTs and cDNAs were downloaded from the TAIR ftp server,
release 7)

genic: 1 if this TAR overlaps (by at least 1 nt) to a gene annotated
in TAIR7, 0 otherwise

nonexonic_length: number of nucleotides inclusive to this TAR that do 
NOT overlap to any annotated exon 

EST_free_length: number of nucleotides inclusive to this TAR that do
NOT overlap to any EST/cDNA alignment

nongenic_length: number of nucleotides inclusive to this TAR that do
NOT overlap to any annotated gene (any of its exons or introns)


Column definition for induced_tars.txt files
---------------------------------------------------------

chr: same as in tars.txt files

start: same as in tars.txt files

stop: same as in tars.txt files

num_probes: same as in tars.txt files

level: same as in tars.txt files

upstr_gene: AGI code of the nearest annotated gene upstream of this
TAR

downstr_gene: AGI code of the nearest annotated gene downstream of
this TAR

upstr_gene_dist: distance in nucleotides to the nearest annotated gene
upstream

downstr_gene_dist: distance in nucleotides to the nearest annotated
gene downstream

p_value: p-value of a Mann-Whitney U test for significantly increased
signal in treatment vs. control arrays (as indicated by the file
name). The test compares the median intensities (pooling replicate
arrays) of all probes inclusive to this TAR between treatment and
control. Lists are cut off at the 5% alpha level.

repeats: same as in tars.txt files

high_confidence: same as in tars.txt files

unannotated: same as in tars.txt files

novel: same as in tars.txt files

genic: same as in tars.txt files

nonexonic_length: same as in tars.txt file

EST_free_length: same as in tars.txt file

nongenic_length: same as in tars.txt file