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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). |
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== Log Base 2 of Normalized Ratios == | == Log Base 2 of Normalized Ratios == | ||
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|1.0954 | |1.0954 | ||
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== Boolean Values (Threshold of 2.0) == | == Boolean Values (Threshold of 2.0) == | ||
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== Boolean Input Functions == | == Boolean Input Functions == | ||
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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>] | ||
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== 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
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.
