Team:CBNU-Korea/Project/GD/Analysis
From 2012.igem.org
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+ | |||
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</head> | </head> | ||
Line 74: | Line 391: | ||
</div> | </div> | ||
<div id="CB_sub_menu"> | <div id="CB_sub_menu"> | ||
- | <ul> | + | <div id="CB_sub_mobile_menu">+ MENU</div> |
+ | <ul class="CB_ul"> | ||
<li class="OVERVIEW"><a | <li class="OVERVIEW"><a | ||
href="https://2012.igem.org/Team:CBNU-Korea/Project">01 + | href="https://2012.igem.org/Team:CBNU-Korea/Project">01 + | ||
Line 82: | Line 400: | ||
+ Brick Designer</a></li> | + Brick Designer</a></li> | ||
<li class="MGD"><a href="#">03 + Minimal Genome Designer</a></li> | <li class="MGD"><a href="#">03 + Minimal Genome Designer</a></li> | ||
- | <li id="li_sub" class="MGD_Overview"><a href=" | + | <li id="li_sub" class="MGD_Overview"><a |
+ | href="https://2012.igem.org/Team:CBNU-Korea/Project/GD/Overview">- | ||
Overview</a></li> | Overview</a></li> | ||
<li id="li_sub" class="MGD_Method"><a | <li id="li_sub" class="MGD_Method"><a | ||
href="https://2012.igem.org/Team:CBNU-Korea/Project/GD/Method">- | href="https://2012.igem.org/Team:CBNU-Korea/Project/GD/Method">- | ||
Method</a></li> | Method</a></li> | ||
- | <li id="li_sub" class="MGD_Analysis"><a | + | <li id="li_sub" class="MGD_Analysis"><a href="#">- |
- | + | ||
Analysis</a></li> | Analysis</a></li> | ||
<li class="DOWNLOAD"><a | <li class="DOWNLOAD"><a | ||
Line 141: | Line 459: | ||
paired of Locus_tag 1 by 1. | paired of Locus_tag 1 by 1. | ||
</p> | </p> | ||
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/igem.org/7/76/CBK_C_001.png"> |
<p> | <p> | ||
Line 154: | Line 472: | ||
is satisfied. Therefore, as a result, 82 complete species | is satisfied. Therefore, as a result, 82 complete species | ||
represent the streptococcus.</p> | represent the streptococcus.</p> | ||
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/igem.org/9/9a/CBK_C_002.png"> |
<p> | <p> | ||
Line 177: | Line 495: | ||
</p> | </p> | ||
+ | <div id="select_img_box"> | ||
+ | <select id="CB_select"> | ||
+ | <option>Streptococcus pyogenes MGAS15252</option> | ||
+ | <option>Streptococcus thermophilus CNRZ1066</option> | ||
+ | <option>Streptococcus thermophilus LMG 18311</option> | ||
+ | <option>Streptococcus pyogenes NZ131</option> | ||
+ | <option>Streptococcus pyogenes MGAS9429</option> | ||
+ | <option>Streptococcus pyogenes MGAS5005</option> | ||
+ | <option>Streptococcus pyogenes str. Manfredo</option> | ||
+ | <option>Streptococcus pyogenes M1 GAS</option> | ||
+ | <option>Streptococcus pyogenes MGAS2096</option> | ||
+ | <option>Streptococcus pyogenes SSI-1</option> | ||
+ | <option>Streptococcus pyogenes MGAS8232</option> | ||
+ | <option>Streptococcus pyogenes MGAS6180</option> | ||
+ | <option>Streptococcus pyogenes MGAS10394</option> | ||
+ | <option>Streptococcus pyogenes MGAS315</option> | ||
+ | <option>Streptococcus pyogenes MGAS10270</option> | ||
+ | <option>Streptococcus pyogenes MGAS10750</option> | ||
+ | <option>Streptococcus infantarius subsp. infantarius | ||
+ | CJ18</option> | ||
+ | <option>Streptococcus suis P1/7</option> | ||
+ | <option>Streptococcus mutans NN2025</option> | ||
+ | <option>Streptococcus equi subsp. zooepidemicus | ||
+ | MGCS10565</option> | ||
+ | <option>Streptococcus mutans UA159</option> | ||
+ | <option>Streptococcus pneumoniae R6</option> | ||
+ | <option>Streptococcus pneumoniae D39</option> | ||
+ | <option>Streptococcus pneumoniae G54</option> | ||
+ | <option>Streptococcus pneumoniae TCH8431/19A</option> | ||
+ | <option>Streptococcus suis SC84</option> | ||
+ | <option>Streptococcus pasteurianus ATCC 43144</option> | ||
+ | <option>Streptococcus dysgalactiae subsp. equisimilis | ||
+ | GGS_124</option> | ||
+ | <option>Streptococcus pneumoniae P1031</option> | ||
+ | <option>Streptococcus pneumoniae Taiwan19F-14</option> | ||
+ | <option>Streptococcus pneumoniae JJA</option> | ||
+ | <option>Streptococcus agalactiae A909</option> | ||
+ | <option>Streptococcus macedonicus ACA-DC 198</option> | ||
+ | <option>Streptococcus pneumoniae AP200</option> | ||
+ | <option>Streptococcus parauberis KCTC 11537</option> | ||
+ | <option>Streptococcus mitis B6</option> | ||
+ | <option>Streptococcus agalactiae 2603V/R</option> | ||
+ | <option>Streptococcus pneumoniae TIGR4</option> | ||
+ | <option>Streptococcus pneumoniae 70585</option> | ||
+ | <option>Streptococcus gordonii str. Challis substr. CH1</option> | ||
+ | <option>Streptococcus pneumoniae CGSP14</option> | ||
+ | <option>Streptococcus agalactiae NEM316</option> | ||
+ | <option>Streptococcus salivarius CCHSS3</option> | ||
+ | <option>Streptococcus pneumoniae ATCC 700669</option> | ||
+ | <option>Streptococcus pneumoniae 670-6B</option> | ||
+ | <option>Streptococcus pneumoniae Hungary19A-6</option> | ||
+ | <option>Streptococcus equi subsp. equi 4047</option> | ||
+ | <option>Streptococcus gallolyticus UCN34</option> | ||
+ | <option>Streptococcus sanguinis SK36</option> | ||
+ | <option>Streptococcus pseudopneumoniae IS7493</option> | ||
+ | <option>Streptococcus suis ST3</option> | ||
+ | <option>Streptococcus oralis Uo5</option> | ||
+ | <option>Streptococcus gallolyticus subsp. gallolyticus | ||
+ | ATCC BAA-2069</option> | ||
+ | <option>Streptococcus suis BM407</option> | ||
+ | <option>Streptococcus equi subsp. zooepidemicus</option> | ||
+ | <option>Streptococcus uberis 0140J</option> | ||
+ | <option>Streptococcus suis 98HAH33</option> | ||
+ | <option>Streptococcus suis 05ZYH33</option> | ||
+ | <option>Streptococcus thermophilus LMD-9</option> | ||
+ | <option>ccus salivarius JIM8777</option> | ||
+ | <option>s pneumoniae SPN034156 draft genome</option> | ||
+ | <option>Streptococcus pneumoniae SPN034183 draft genome</option> | ||
+ | <option>Streptococcus pneumoniae SPN033038 draft genome</option> | ||
+ | <option>Streptococcus pneumoniae SPN032672 draft genome</option> | ||
+ | <option>Streptococcus pneumoniae INV104 genome</option> | ||
+ | <option>Streptococcus pneumoniae INV200 genome</option> | ||
+ | <option>Streptococcus pneumoniae OXC141 genome</option> | ||
+ | <option>Streptococcus pneumoniae ST556</option> | ||
+ | <option>Streptococcus pyogenes MGAS1882</option> | ||
+ | <option>Streptococcus pyogenes Alab49</option> | ||
+ | <option>Streptococcus equi subsp. zooepidemicus ATCC | ||
+ | 35246</option> | ||
+ | <option>Streptococcus salivarius 57.I</option> | ||
+ | <option>Streptococcus suis ST1</option> | ||
+ | <option>Streptococcus suis D12</option> | ||
+ | <option>Streptococcus suis D9</option> | ||
+ | <option>Streptococcus suis SS12</option> | ||
+ | <option>Streptococcus suis A7</option> | ||
+ | <option>Streptococcus suis JS14</option> | ||
+ | <option>Streptococcus thermophilus ND03</option> | ||
+ | <option>Streptococcus dysgalactiae subsp. equisimilis | ||
+ | ATCC 12394</option> | ||
+ | <option>Streptococcus suis GZ1</option> | ||
+ | <option>Streptococcus gallolyticus subsp. gallolyticus | ||
+ | ATCC 43143 DNA</option> | ||
+ | </select> | ||
+ | |||
+ | <div id="CB_sub_chart_1"></div> | ||
+ | <div id="CB_sub_chart_2"></div> | ||
+ | </div> | ||
<h2>2-2. Analysis</h2> | <h2>2-2. Analysis</h2> | ||
<p> | <p> | ||
<strong>1) Strand</strong> | <strong>1) Strand</strong> | ||
</p> | </p> | ||
- | |||
<p>- We chose 77 species out of 82 species randomly, and | <p>- We chose 77 species out of 82 species randomly, and | ||
estimated the patterns of the strand ratio of each sections, and | estimated the patterns of the strand ratio of each sections, and | ||
Line 187: | Line 600: | ||
<p>- We checked the strand ratio of the essential gene.</p> | <p>- We checked the strand ratio of the essential gene.</p> | ||
- | <p> | + | <p> |
- | <p>- We checked where the genome is distributed.</p> | + | <strong>2) Region</strong> |
+ | </p> | ||
+ | <p>- We found the COG and the frequency of the essential gene | ||
+ | because of referred to the genome design</p> | ||
+ | <p> | ||
+ | 2-1) We checked where the essential genome is distributed.<br>2-2) | ||
+ | We checked where the gene by being provided COG is distributed. | ||
+ | </p> | ||
Line 198: | Line 618: | ||
genes were distributed in 4 places with different tendency. So we | genes were distributed in 4 places with different tendency. So we | ||
decided the section of the proc transreg as 4, and analyzed.</p> | decided the section of the proc transreg as 4, and analyzed.</p> | ||
- | < | + | |
+ | |||
+ | |||
+ | <div id="select_img_box"> | ||
+ | <select id="CB_select2"> | ||
+ | <option>Streptococcus pyogenes MGAS15252</option> | ||
+ | <option>Streptococcus thermophilus CNRZ1066</option> | ||
+ | <option>Streptococcus thermophilus LMG 18311</option> | ||
+ | <option>Streptococcus pyogenes NZ131</option> | ||
+ | <option>Streptococcus pyogenes MGAS9429</option> | ||
+ | <option>Streptococcus pyogenes MGAS5005</option> | ||
+ | <option>Streptococcus pyogenes str. Manfredo</option> | ||
+ | <option>Streptococcus pyogenes M1 GAS</option> | ||
+ | <option>Streptococcus pyogenes MGAS2096</option> | ||
+ | <option>Streptococcus pyogenes SSI-1</option> | ||
+ | <option>Streptococcus pyogenes MGAS8232</option> | ||
+ | <option>Streptococcus pyogenes MGAS6180</option> | ||
+ | <option>Streptococcus pyogenes MGAS10394</option> | ||
+ | <option>Streptococcus pyogenes MGAS315</option> | ||
+ | <option>Streptococcus pyogenes MGAS10270</option> | ||
+ | <option>Streptococcus pyogenes MGAS10750</option> | ||
+ | <option>Streptococcus infantarius subsp. infantarius | ||
+ | CJ18</option> | ||
+ | <option>Streptococcus suis P1/7</option> | ||
+ | <option>Streptococcus mutans NN2025</option> | ||
+ | <option>Streptococcus equi subsp. zooepidemicus | ||
+ | MGCS10565</option> | ||
+ | <option>Streptococcus mutans UA159</option> | ||
+ | <option>Streptococcus pneumoniae R6</option> | ||
+ | <option>Streptococcus pneumoniae D39</option> | ||
+ | <option>Streptococcus pneumoniae G54</option> | ||
+ | <option>Streptococcus pneumoniae TCH8431/19A</option> | ||
+ | <option>Streptococcus suis SC84</option> | ||
+ | <option>Streptococcus pasteurianus ATCC 43144</option> | ||
+ | <option>Streptococcus dysgalactiae subsp. equisimilis | ||
+ | GGS_124</option> | ||
+ | <option>Streptococcus pneumoniae P1031</option> | ||
+ | <option>Streptococcus pneumoniae Taiwan19F-14</option> | ||
+ | <option>Streptococcus pneumoniae JJA</option> | ||
+ | <option>Streptococcus agalactiae A909</option> | ||
+ | <option>Streptococcus macedonicus ACA-DC 198</option> | ||
+ | <option>Streptococcus pneumoniae AP200</option> | ||
+ | <option>Streptococcus parauberis KCTC 11537</option> | ||
+ | <option>Streptococcus mitis B6</option> | ||
+ | <option>Streptococcus agalactiae 2603V/R</option> | ||
+ | <option>Streptococcus pneumoniae TIGR4</option> | ||
+ | <option>Streptococcus pneumoniae 70585</option> | ||
+ | <option>Streptococcus gordonii str. Challis substr. CH1</option> | ||
+ | <option>Streptococcus pneumoniae CGSP14</option> | ||
+ | <option>Streptococcus agalactiae NEM316</option> | ||
+ | <option>Streptococcus salivarius CCHSS3</option> | ||
+ | <option>Streptococcus pneumoniae ATCC 700669</option> | ||
+ | <option>Streptococcus pneumoniae 670-6B</option> | ||
+ | <option>Streptococcus pneumoniae Hungary19A-6</option> | ||
+ | <option>Streptococcus equi subsp. equi 4047</option> | ||
+ | <option>Streptococcus gallolyticus UCN34</option> | ||
+ | <option>Streptococcus sanguinis SK36</option> | ||
+ | <option>Streptococcus pseudopneumoniae IS7493</option> | ||
+ | <option>Streptococcus suis ST3</option> | ||
+ | <option>Streptococcus oralis Uo5</option> | ||
+ | <option>Streptococcus gallolyticus subsp. gallolyticus | ||
+ | ATCC BAA-2069</option> | ||
+ | <option>Streptococcus suis BM407</option> | ||
+ | <option>Streptococcus equi subsp. zooepidemicus</option> | ||
+ | <option>Streptococcus uberis 0140J</option> | ||
+ | <option>Streptococcus suis 98HAH33</option> | ||
+ | <option>Streptococcus suis 05ZYH33</option> | ||
+ | <option>Streptococcus thermophilus LMD-9</option> | ||
+ | <option>ccus salivarius JIM8777</option> | ||
+ | <option>s pneumoniae SPN034156 draft genome</option> | ||
+ | <option>Streptococcus pneumoniae SPN034183 draft genome</option> | ||
+ | <option>Streptococcus pneumoniae SPN033038 draft genome</option> | ||
+ | <option>Streptococcus pneumoniae SPN032672 draft genome</option> | ||
+ | <option>Streptococcus pneumoniae INV104 genome</option> | ||
+ | <option>Streptococcus pneumoniae INV200 genome</option> | ||
+ | <option>Streptococcus pneumoniae OXC141 genome</option> | ||
+ | <option>Streptococcus pneumoniae ST556</option> | ||
+ | <option>Streptococcus pyogenes MGAS1882</option> | ||
+ | <option>Streptococcus pyogenes Alab49</option> | ||
+ | <option>Streptococcus equi subsp. zooepidemicus ATCC | ||
+ | 35246</option> | ||
+ | <option>Streptococcus salivarius 57.I</option> | ||
+ | <option>Streptococcus suis ST1</option> | ||
+ | <option>Streptococcus suis D12</option> | ||
+ | <option>Streptococcus suis D9</option> | ||
+ | <option>Streptococcus suis SS12</option> | ||
+ | <option>Streptococcus suis A7</option> | ||
+ | <option>Streptococcus suis JS14</option> | ||
+ | <option>Streptococcus thermophilus ND03</option> | ||
+ | <option>Streptococcus dysgalactiae subsp. equisimilis | ||
+ | ATCC 12394</option> | ||
+ | <option>Streptococcus suis GZ1</option> | ||
+ | <option>Streptococcus gallolyticus subsp. gallolyticus | ||
+ | ATCC 43143 DNA</option> | ||
+ | </select> | ||
+ | |||
+ | <div id="CB_sub_chart_3"></div> | ||
+ | </div> | ||
+ | |||
+ | |||
<p> | <p> | ||
Line 209: | Line 728: | ||
significance level of 0.01, the null hypothesis is dismissible. In | significance level of 0.01, the null hypothesis is dismissible. In | ||
other words, the regression model is more suitable.</p> | other words, the regression model is more suitable.</p> | ||
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/igem.org/5/5f/CBK_C_003.png"> |
<p> | <p> | ||
Line 215: | Line 734: | ||
</p> | </p> | ||
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/igem.org/0/01/CBK_C_004.png"> |
<p>As the notable probability gets smaller, it can affect the | <p>As the notable probability gets smaller, it can affect the | ||
Line 242: | Line 761: | ||
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/igem.org/d/d2/CBK_C_005.png"> |
<p>The X axis shows the 100 sections of the genome of the | <p>The X axis shows the 100 sections of the genome of the | ||
Line 256: | Line 775: | ||
</p> | </p> | ||
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/igem.org/d/df/CBK_C_006.png"> |
<p>By conducting the chi-square test with the estimated | <p>By conducting the chi-square test with the estimated | ||
transpose linear regression prediction equation with the 77 | transpose linear regression prediction equation with the 77 | ||
Line 277: | Line 796: | ||
</p> | </p> | ||
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/igem.org/3/33/CBK_C_007.png"> <img |
+ | src="https://static.igem.org/mediawiki/igem.org/b/ba/CBK_C_008.png"> | ||
- | <p>As a result to guess the distribution of the essential gene, | + | <p>The X axis shows the 20 sections of the genome size. And the |
- | + | Y axis is the frequency of the genome. As a result to guess the | |
- | + | distribution of the essential gene, the graph is showed like that. | |
- | + | We know that 322 essential genes among 485 essential gene are | |
- | + | distributed a bilateral symmetry in the middle of origin. We can | |
- | + | divide between the Synb_ID which is the origin of high frequency | |
+ | and Synb_ID which is the origin of high frequency by both sides.</p> | ||
<p> | <p> | ||
Line 291: | Line 812: | ||
</p> | </p> | ||
- | <img src=""> | + | <img src="https://static.igem.org/mediawiki/igem.org/1/15/CBK_C_009.png"> <img |
- | + | src="https://static.igem.org/mediawiki/igem.org/5/57/CBK_C_010.png"> <img | |
- | + | src="https://static.igem.org/mediawiki/igem.org/7/74/CBK_C_011.png"> <img | |
+ | src="https://static.igem.org/mediawiki/igem.org/b/b2/CBK_C_012.png"> | ||
+ | <p> | ||
+ | The X axis shows the 20 sections of the genome size. And the Y | ||
+ | axis is the frequency of the gene provided the COG.<br> As a | ||
+ | result to guess the distribution of gene by being provided COG, | ||
+ | the graph provide an information that the COG is distributed | ||
+ | symmetrically around the middle of origin. | ||
+ | </p> | ||
</div> | </div> | ||
</div> | </div> |
Latest revision as of 00:48, 27 September 2012
Minimal Genome Designer
- Analysis
![](https://static.igem.org/mediawiki/2012/6/6e/CBK_overlay_001.png)
1. Introduction
1-1. Suggestion
Since the Genome project started in 2002, we can easily get the genetic information of many species. Also as the scientific technique developed, we can insert and compose the genome. If we can design a whole genome, then we will be able to make a one and only useful genome. But as today, the compose of the minimum genome made with the essential gene has succeeded, but did not last.
1-2. Object
To design a genome, we have to analyze the pattern of the genome and the distribution of the gene.
1-3. Method and the range of the study
The study was used information of species in streptococcus by
patric database (
http://www.patricbrc.org/portal/portal/patric/Home) and SynbUID.
The Data was built by mysql 5.5.27, and a statistical analysis
program was used by SAS 9.3.
2. Design
2-1. Prepare
1) Build database
An attribute of Genome name is consisted of ID, Genome_name, COG,
Start, End, Strand, and Size.
An attribute of Annotation
Table_EG is consisted of ID, locus, and SynbUID. Two entities are
paired of Locus_tag 1 by 1.
![](https://static.igem.org/mediawiki/igem.org/7/76/CBK_C_001.png)
2) Represented sample number
For checking the number of specimen that is representative, we used a simple random sampling method, and assumed that the complete genome is random. We used the significance level (a=0.05) and the limit of error (b=0.1). The total species of streptococcus is 494 species, and between these, 82 species are completed. According to our calculation, when there is 81 species, the result is satisfied. Therefore, as a result, 82 complete species represent the streptococcus.
![](https://static.igem.org/mediawiki/igem.org/9/9a/CBK_C_002.png)
3) Standard
3-1) Divided the interval of the genome
The number and size of the genome differs between species. To supplement this problem, we divided the genes in a section to show the genome’s size as a proportion. As a result, when we divided the analyzing section less then a hundred, it was hard to see the patterns because the data has been diluted. And when we divided it into more then a hundred pieces, it was not that different from the result that divided it into a hundred pieces. So we decided to divide it into a hundred pieces.
3-2) Identified the starting point
The number one ORF of each gene sequence analysis data is different between every species. Thus we had to make a specific standard to equalize the beginning of the data. We checked the strand pattern of each genome and identified it with the strands.
2-2. Analysis
1) Strand
- We chose 77 species out of 82 species randomly, and estimated the patterns of the strand ratio of each sections, and verified the estimated number with the other 5 species.
- We checked the strand ratio of the essential gene.
2) Region
- We found the COG and the frequency of the essential gene because of referred to the genome design
2-1) We checked where the essential genome is distributed.
2-2)
We checked where the gene by being provided COG is distributed.
3. Result
2-1. Strand
When we checked the strand pattern of the 82 species, the genes were distributed in 4 places with different tendency. So we decided the section of the proc transreg as 4, and analyzed.
1) Estimated the transpose linear regression
We explained with a theory that ‘The null hypothesis does not satisfy the regression model, but the alternative hypothesis does.’ As a result in the SAS, according to the null hypothesis, the F-value was 3093.13, and the P=value <.0001. Therefore at a significance level of 0.01, the null hypothesis is dismissible. In other words, the regression model is more suitable.
![](https://static.igem.org/mediawiki/igem.org/5/5f/CBK_C_003.png)
2) Estimated factor β0, β1
![](https://static.igem.org/mediawiki/igem.org/0/01/CBK_C_004.png)
As the notable probability gets smaller, it can affect the dependent variable more. According to the null hypothesis, the F-value of β0 is 10.13, and the Pr > F 0.0015. So the null hypothesis is dismissable. And the estimated calculation is 1.22744031. Also F-value of β1 was 3093.13, and the Pr > F <.0001, so again the null hypothesis is dismissed. Therefore, the estimated number is 0.97546498.
3) Estimated the transe regression model
As a result to look the distribution of the strand to each
species, we found a similar pattern. Thus we studied the pattern
of the strand distribution after to range a standard by section
which is changed the strand's sign. By using The Transpose
Regression Method, we have a result to be able to express The
Spline Regression Model by the distribution pattern of the strand
of 82 species.
Identity(spercent) = 1.22744031
+ 0.97546498*spline(interval)
![](https://static.igem.org/mediawiki/igem.org/d/d2/CBK_C_005.png)
The X axis shows the 100 sections of the genome of the randomly selected 77 species. And the Y axis is the ratio of the + patterns of each section. The sum of each section’s +, - pattern is 100. According to the graph above, when the standard number is 50, the + patterns appears as 25 on the left, and the – pattern on the right higher than 80. So in this case, it is a + pattern.
4) Verifying the estimated Prediction Equation is adequate.
![](https://static.igem.org/mediawiki/igem.org/d/df/CBK_C_006.png)
By conducting the chi-square test with the estimated transpose linear regression prediction equation with the 77 randomly selected species, we verified if the equation is adequate. The null hypothesis is independent from the prediction equation and the other 5 species that was not selected. And the alternative hypothesis is subordinate with the prediction equation and the 5 species. The p-value of the 5 species is independent from the prediction equation estimated by the null hypothesis. We can see that it is subordinate when it is dismissed.
2-2. Region
We estimated the origin which is a part of changed strand’s pattern.
1) The spread of the essential genes is shown at the table below.
![](https://static.igem.org/mediawiki/igem.org/3/33/CBK_C_007.png)
![](https://static.igem.org/mediawiki/igem.org/b/ba/CBK_C_008.png)
The X axis shows the 20 sections of the genome size. And the Y axis is the frequency of the genome. As a result to guess the distribution of the essential gene, the graph is showed like that. We know that 322 essential genes among 485 essential gene are distributed a bilateral symmetry in the middle of origin. We can divide between the Synb_ID which is the origin of high frequency and Synb_ID which is the origin of high frequency by both sides.
2) The spread of the genes provided COG is shown at the table below.
![](https://static.igem.org/mediawiki/igem.org/1/15/CBK_C_009.png)
![](https://static.igem.org/mediawiki/igem.org/5/57/CBK_C_010.png)
![](https://static.igem.org/mediawiki/igem.org/7/74/CBK_C_011.png)
![](https://static.igem.org/mediawiki/igem.org/b/b2/CBK_C_012.png)
The X axis shows the 20 sections of the genome size. And the Y
axis is the frequency of the gene provided the COG.
As a
result to guess the distribution of gene by being provided COG,
the graph provide an information that the COG is distributed
symmetrically around the middle of origin.