Team:Nevada/Original Data

From 2010.igem.org

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== Original Data Set ==
== Original Data Set ==
-
Data collected from microarray experiments performed by Jian-Kang Zhu, ''et al,'' and published on the Gene Expression Omnibus database (Zhu, ''et al'').  
+
Data collected from microarray experiments performed by Jian-Kang Zhu, ''et al,'' and published on the Gene Expression Omnibus database (Zhu, ''et al.'' 2005).  
{| border="3"
{| border="3"
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|1599.3
|1599.3
|125
|125
 +
|}
 +
<br>
 +
<br>
 +
<br>
== Log Base 2 of Normalized Ratios ==
== Log Base 2 of Normalized Ratios ==
-
Table
+
Values were normalized to 1 at t0, and log base 2 values were taken.
 +
 
 +
{| border="3"
 +
|Log2 Ratios
 +
|ICE1
 +
|DREB1A
 +
|DREB1B
 +
|DREB1C
 +
|RD29A
 +
|ZAT6
 +
|RAP2.1
 +
|RAP2.6
 +
|-
 +
|t0
 +
|0
 +
|0
 +
|0
 +
|0
 +
|0
 +
|0
 +
|0
 +
|0
 +
|-
 +
|t1
 +
|0.1315
 +
|5.9666
 +
|7.6221
 +
|7.4107
 +
|1.1219
 +
|2.2186
 +
|0.0425
 +
| -0.0299
 +
|-
 +
|t2
 +
|0.1887
 +
|5.9997
 +
|7.3863
 +
|7.3407
 +
|2.8182
 +
|3.4794
 +
|1.8334
 +
| -0.1616
 +
|-
 +
|t3
 +
|0.1206
 +
|3.9107
 +
|5.0567
 +
|6.0222
 +
|3.6347
 +
|4.2942
 +
|3.9936
 +
|1.0954
 +
|}
 +
<br>
 +
<br>
 +
<br>
== Boolean Values (Threshold of 2.0) ==
== Boolean Values (Threshold of 2.0) ==
-
Table
+
Values from the log base 2 table which were greater than or equal to a 2.0-fold increase were assigned values of 1 ( "on" ) and values under 3.5 were assigned values of 0 ( "off" ).
 +
 
 +
{| border="3"
 +
|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
 +
|1
 +
|0
 +
|0
 +
|-
 +
|t2
 +
|0
 +
|1
 +
|1
 +
|1
 +
|1
 +
|1
 +
|0
 +
|0
 +
|-
 +
|t3
 +
|0
 +
|1
 +
|1
 +
|1
 +
|1
 +
|1
 +
|1
 +
|0
 +
|}
 +
<br>
 +
<br>
 +
<br>
== Boolean Input Functions ==
== Boolean Input Functions ==
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The number of Boolean inputs for this data amounted to 20 megabytes worth of text files, and thus, has been omitted.  The extremely large number of inputs going into each gene indicated that the process needed some refinement to limit the number of possible interactions between these genes.  This lead to the data interpolation and limiting the Boolean inputs to being no greater than 4 for each gene.
The number of Boolean inputs for this data amounted to 20 megabytes worth of text files, and thus, has been omitted.  The extremely large number of inputs going into each gene indicated that the process needed some refinement to limit the number of possible interactions between these genes.  This lead to the data interpolation and limiting the Boolean inputs to being no greater than 4 for each gene.
-
For some examples of Boolean Input Functions, please see the [https://2010.igem.org/Team:Nevada/Interpolated_Data|<u>interpolated data page.</u>]
+
For some examples of Boolean Input Functions, please see the [https://2010.igem.org/Team:Nevada/Interpolated_Data<u>interpolated data page.</u>]
 +
<br>
 +
<br>
 +
<br>
== References ==
== References ==
-
Zhu, J-K., Lee, B., Henderson, D. (2005) The Arabidopsis Cold-Responsive Transcriptome and Its Regulation by ICE1. ''Plant Cell.'' Vol. 17, Issue 11, p3155-3175.
+
'''Zhu, J-K., Lee, B., Henderson, D.''' (2005) The Arabidopsis Cold-Responsive Transcriptome and Its Regulation by ICE1. ''Plant Cell.'' Vol. 17, Issue 11, p3155-3175.

Latest revision as of 19:43, 27 October 2010

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Contents

Original Data Set

Data collected from microarray experiments performed by Jian-Kang Zhu, et al, and published on the Gene Expression Omnibus database (Zhu, et al. 2005).

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 1487.7 6041 4826.5 11809.1 3284.5 676.3 103.4 57.3
t2 1547.9 6181.2 4099 11249.3 10644.4 1620.6 357.8 52.3
t3 1476.5 1452.8 815.4 4510.4 18745.9 2850.7 1599.3 125




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 0.1315 5.9666 7.6221 7.4107 1.1219 2.2186 0.0425 -0.0299
t2 0.1887 5.9997 7.3863 7.3407 2.8182 3.4794 1.8334 -0.1616
t3 0.1206 3.9107 5.0567 6.0222 3.6347 4.2942 3.9936 1.0954




Boolean Values (Threshold of 2.0)

Values from the log base 2 table which were greater than or equal to a 2.0-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 1 0 0
t2 0 1 1 1 1 1 0 0
t3 0 1 1 1 1 1 1 0




Boolean Input Functions

The number of Boolean inputs for this data amounted to 20 megabytes worth of text files, and thus, has been omitted. The extremely large number of inputs going into each gene indicated that the process needed some refinement to limit the number of possible interactions between these genes. This lead to the data interpolation and limiting the Boolean inputs to being no greater than 4 for each gene.

For some examples of Boolean Input Functions, please see the interpolated data page.


References

Zhu, J-K., Lee, B., Henderson, D. (2005) The Arabidopsis Cold-Responsive Transcriptome and Its Regulation by ICE1. Plant Cell. Vol. 17, Issue 11, p3155-3175.
Retrieved from "http://2010.igem.org/Team:Nevada/Original_Data"