Team:Nevada/Interpolated Data

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== Boolean Input Functions ==
== Boolean Input Functions ==

Revision as of 08:24, 27 October 2010

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Contents

Interpolation Method

Natural cubic splines were made based on the four time points for each gene. This produced 3 polynomials, for each gene, defining their time states: one for the interval from 0 to 3 hours, the second from 3 to 6 hours and the third from 6 to 24 hours. For all genes, the third polynomial was also used to extrapolate out to 30 hours, in order to get a sense of whether or not some of these genes may have a delayed response to freezing. 16 time points were taken from the 30-hour interpolated/extrapolated data at 2 hour intervals to produce this data set, i.e. ( t0 = 0 hours, t1 = 2 hours, t2 = 4 hours...t15 = 30 hours ).


Interpolated Data Set

Raw Data ICE1 DREB1A DREB1B DREB1C rd29A ZAT6 RAP2.1 RAP2.6
t0 1358.1 96.6 24.5 69.4 1509.2 145.3 100.4 58.5
t1 1450.6 4600.5 3748.3 9051.6 2125.8 455.4 78.4 58.2
t2 1515 6617.4 5072.8 12724.1 5330.4 965.3 166.6 55.8
t3 1547.9 6181.2 4099 11249.3 10644.4 1620.6 357.8 52.3
t4 1566.7 5400.5 2970.9 9273.8 15161.9 2168.8 549.6 51.6
t5 1576.1 4709.9 2112.2 7731.3 18402.6 2571.8 722.5 53.9
t6 1577.2 4098.1 1489.2 6567.6 20526.3 2847.7 878.6 59
t7 1571.2 3554 1068.2 5728.6 21692.4 3014.6 1020.5 66.4
t8 1559.4 3066.1 815.6 5160.2 22060.6 3090.8 1150.5 75.8
t9 1542.8 2623.4 697.7 4808.4 21790.5 3094.3 1271.1 86.8
t10 1522.6 2214.4 680.8 4618.8 21041.6 3043.4 1384.4 98.9
t11 1500.2 1828 731.3 4537.6 19973.6 2956.1 1493.7 111.8
t12 1476.5 1452.8 815.4 4510.4 18745.9 2850.7 1599.3 125
t13 1452.8 1077.6 899.5 4483.2 17518.2 2745.3 1705.5 138.3
t14 1430.4 691.2 950 4402 16450.2 2658 1814.2 151.1
t15 1410.2 282.2 933.1 4212.4 15701.3 2607.1 1927.5 163.2




Log Base 2 of Normalized Ratios

Values were normalized to 1 at t0, and log base 2 values were taken.

Log2 Ratios ICE1 DREB1A DREB1B DREB1C rd29A ZAT6 RAP2.1 RAP2.6
t0 0 0 0 0 0 0 0 0
t1 0.0951 5.5736 7.2573 7.0271 0.4942 1.6481 -0.3568 -0.0074
t2 0.1577 6.0981 7.6939 7.5184 1.8205 2.7319 0.7306 -0.0682
t3 0.1887 5.9997 7.3863 7.3407 2.8182 3.4794 1.8334 -0.1616
t4 0.2061 5.8049 6.9220 7.0621 3.3286 3.8998 2.4526 -0.1811
t5 0.2148 5.6075 6.4298 6.7996 3.6081 4.1457 2.8472 -0.1182
t6 0.2158 5.4068 5.9256 6.5643 3.7656 4.2927 3.1294 0.0123
t7 0.2103 5.2013 5.4463 6.3671 3.8453 4.3749 3.3454 0.1827
t8 0.1994 4.9882 5.0570 6.2163 3.8696 4.4109 3.5184 0.3738
t9 0.1840 4.7633 4.8318 6.1145 3.8518 4.4125 3.6622 0.5693
t10 0.1649 4.5187 4.7964 6.0564 3.8014 4.3886 3.7854 0.7575
t11 0.1436 4.2421 4.8996 6.0308 3.7262 4.3466 3.8951 0.9344
t12 0.1206 3.9107 5.0567 6.0222 3.6347 4.2942 3.9936 1.0954
t13 0.0972 3.4797 5.1983 6.0134 3.5370 4.2399 4.0864 1.2413
t14 0.0748 2.8390 5.2771 5.9871 3.4462 4.1932 4.1755 1.3690
t15 0.0543 1.5466 5.2512 5.9236 3.3790 4.1653 4.2629 1.4801




Boolean Values (Threshold of 3.5)

Values from the log base 2 table which were greater than or equal to a 3.5-fold increase were assigned values of 1 ( "on" ) and values under 3.5 were assigned values of 0 ( "off" ).

Boolean Values ICE1 DREB1A DREB1B DREB1C RD29A ZAT6 RAP2.1 RAP2.6
t0 0 0 0 0 0 0 0 0
t1 0 1 1 1 0 0 0 0
t2 0 1 1 1 0 0 0 0
t3 0 1 1 1 0 0 0 0
t4 0 1 1 1 0 1 0 0
t5 0 1 1 1 1 1 0 0
t6 0 1 1 1 1 1 0 0
t7 0 1 1 1 1 1 0 0
t8 0 1 1 1 1 1 1 0
t9 0 1 1 1 1 1 1 0
t10 0 1 1 1 1 1 1 0
t11 0 1 1 1 1 1 1 0
t12 0 1 1 1 1 1 1 0
t13 0 0 1 1 1 1 1 0
t14 0 0 1 1 0 1 1 0
t15 0 0 1 1 0 1 1 0




Boolean Input Functions

When reading the true Boolean outputs, the first number in a line gives the number of inputs for that gene. Subsequent numbers indicate the genes contributing to the true function. Logical operators are: ( - = NOT ), ( & = AND ), ( | = OR ).

Gene numbers corresponding to the 8 genes are as follows:

1 = ICE1
2 = DREB1A
3 = DREB1B
4 = DREB1C
5 = rd29A
6 = ZAT6
7 = RAP2.1
8 = RAP2.6

As an example of a true Boolean function, consider:

4 ( -1 | 3 ) & ( 5 ) & ( 6 )

This means that the selected gene has four inputs with true values, and those inputs are ( ( NOT ICE1 ) OR DREB1B ) AND ( rd29A ) AND ( ZAT6 ).





For these functions, inputs were limited to 4 per gene. This, in conjunction with increasing the number of time points to take values from, dramatically reduced the number of Boolean input functions in all cases. However, ICE1 and RAP2.6 were still associated with billions of functions. Both of these genes share identical expression profiles ( "off" at all time points ) and identical input functions. For ICE1, this is due to post-transcriptional regulation and being active even though transcript levels remain constant under cold-stress, but it is unknown if RAP2.6 is post-transcriptionally modified. Because of the unwieldy number of input functions for ICE1 and RAP2.6, data has again been omitted for these genes.

Note also that DREB1A, ZAT6 and RAP2.1 do not appear in the list. This is because these genes had no possible inputs associated with them. This does not preclude them from appearing as inputs for the five other genes though.