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Supplementary Table 1. Gene Enrichment Analysis of modified HMPR and UF libraries.
Databases
MAGIv4.0 contigs and
singletons‡
MAGIv4.0 contigs§
MAGIv4.0 contigs
genes¶
DFCI maize gene
index#
Total maize nuclear
B73 Husk
No.
%†
244,189
52.2
Modified HMPR
B73 Root
No.
%
131,398
61.2
Mo17 Root
No.
%
822,117
67.0
207,576
129,095
44.4
27.6
118,367
75,453
55.1
35.1
784,094
501,116
75,027
16.0
44,454
20.7
467,646
100.0
214,782
100.0
†
UF
No.
124,323
%
25.2
61.0
40.8
87,387
41,004
17.7
8.3
317,016
25.8
23,124
4.7
1,227,191
100.0
493,590
100.0
The total number of sequences in each category expressed as a percentage of the total of maize nuclear
(repeat + non-repeat) sequences. A sequence was defined as having a significant match to a
sequence in one of the databases if identity was greater than 95% over a length of at least 40 bp
with an expect value less than or equal to 10-10 using BLAT.
‡
Maize Assembled Genome Island Version 4.0 (MAGIv4.0) contigs and singletons database is a partial
maize genome assembly of B73 genomic sequences (Kalyanaraman et al. 2007)
(http://magi.plantgenomics.iastate.edu/).
§
MAGIv4.0 contigs database differs from the MAGIv4.0 contigs and singletons database in that it only
contains consensus sequences derived from two or more overlapping reads.
¶
MAGIv4.0 contigs genes database consists of 61,428 pre-mature mRNA gene structures that were
predicted via running FGENESH v2.6 on the 163,390 MAGIv4.0 contig sequences. Gene
structures consist of predicted UTRs, exons, and introns. In addition, the predicted gene
structures are bordered by 300 bases upstream and downstream of the predicted transcription
initiation and termination sites, respectively (http://magi.plantgenomics.iastate.edu/).
#
The DFCI maize gene index (ZMGI release 17.0) consists of 115,744 unique expressed maize transcript
sequences (http://compbio.dfci.harvard.edu).
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