My Summer Life in My Summer Life in ChicagoChicago

University of Chicago

Lab. of prof. Wen-Hsiung Li

This summer, I was there…

891605 生科 04G 蔡彝帆

I. Summer ResearchI. Summer Research

Duplicate genes in YeastDuplicate genes in Yeast

蔡彝帆 (I-fan Tsai)

周逸民 (Albert Chou)

2002.11.1

名詞解釋名詞解釋Duplicated GeneCodon usage example UCU UCC UCA Ser UCGCodon usage biasENC 用來表示 codon usage bias 的一個 index Value: from 20~61(stop:UGA UAA UAG)

There’s something There’s something interestinginteresting

There are two similar genes in an organism.

Only one of them has it’s original function, and the other one may be more and more different from the original one.

Function Change → Codon usage bias change

There’s something interesting in

codon usage bias in duplicated genes

Expression vs. Codon usage Expression vs. Codon usage biasbias

How is the relationship between codon usage bias and gene expression with the same family

DataData::

a. Gene families: Big gene family 2 gene family All independent pairs

b. Expression data: measurement from Affymetrix microarray

Big gene family

expression v.s. ENC

-2000

0

2000

4000

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20 30 40 50 60

ENC

expr

ession

22_1

23_1

23_2

29_1

32_1

Group_id r2 P value

22_1 0.2615 1.50E-02

23_1 0.8044 6.86E-09

23_2 0.4557 4.09E-04

29_1 0.4765 3.41E-05

32_1 0.1076 6.67E-02

r & p value of each group

Within the same gene family:

High gene expression ←→ small ENC ←→large codon usage bias

- The relationship between expression & ENC is not completely linear.- We can find the correlated degree from r2 & p value.- Linear correlation: 23_1 > 29_1 > 23_2 > 22_1 > 32_1

See other gene families

2 gene family2 gene family

Expression vs. ENC

-10000

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10000

20000

30000

20 30 40 50 60

ENC

Expr

essio

n

All gene familyAll gene family

expression vs. ENC

-5000

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20 30 40 50 60

ENC

expr

ession

In 2 and all gene family: High expression genes←→ large codon usage bias

If we divide each figure into two part

- higher expression genes - lower expression genesfind-lower expression genes←→larger range of ENC value -higher expression genes ←→smaller range of ENC valuei.e, The relationship between gene expression and codon usage bias in lower expressions genes is not as strong as in higher expression genes.

High Expression ←→large codon usage bias

Large expression ←→ Large codon usage bias△ △?

New Question

△△Expression vs. △Codon Expression vs. △Codon usage biasusage bias

Normalized?

2 gene family2 gene family

Expression diff.= higher expression-lower expression

ENC diff.: The corresponding ENC difference between gene pairs.

expression vs. ENC y = -1.8053x + 0.7674R2 = 0.162

p value=1.1E-09

0

0.5

1

1.5

2

2.5

-0.8 -0.6 -0.4 -0.2 0 0.2 0.4

norm. ENC diff.

norm

. exp

ress

ion

diff.

All gene familyAll gene family

expression vs. ENCy = -1.7428x + 0.8773

R2 = 0.148

p valaue=5.88E-27

0

0.5

1

1.5

2

2.5

-0.8 -0.6 -0.4 -0.2 0 0.2 0.4

norm. ENC diff.

norm

. ex

pres

sion

diff.

2 gene family All gene family

ENC diff.< 0 55.95% 58.47%

ENC diff.= 0 1.32% 1.48%

ENC diff.> 0 42.73% 40.05%

Large gene expression ←→ Large codon △ △usage bias

But NOT all gene expression↑ ←→ codon usage bias↑

We can know that gene expression↑do not correspond to codon usage bias↑certainly. But if the codon usage bias increase a lot, it is very possibly that gene expression increase.

But since high gene expression ←→large codon usage bias

Why does gene expression increasing NOT always correspond to codon usage bias increasing?

We think the answer is that the positive relationship between expression & condon usage bias is more significant in high expression genes.

The reason why we think so is that high expression genes have more possibility of translation, so the relationship between codon usage bias and tRNA abundance is stronger.

Is this right?

The average of normalized ENC difference

High expression genes

Low expression genes

All gene family -0.00743 -0.0026

2 gene family -0.01139 -0.00928

• High expression genes: the genes that have higher expression than the average expression of the front 25% genes.

• The average of norm. ENC diff. is count by the gene pairs that the two genes in it are both High expression genes.

• Low expression genes

We can find that high expression genes have smaller ENC diff. Value(i.e, larger codon usage bias).

It says that our assumption may be right, but the differences between high and low expression genes are too small, we think it must has other reasons to cause such a result.

To find what would affect the codon usage bias except gene expression ( tRNA abundant ) is our future work.

Future Work

II. Some FeelingsII. Some Feelings

2002.7.3

拖著沉重的行李，終於，踏上了這片陌生的土地

其實…心裡…是有那麼些不安…

面臨， 2 個月的未知

2002.7.4

第一次逛進 Chicago 市區

走在密西根大道

習慣性的抬著頭走路

為得是 追尋直達天際的大廈的終點

我想 ~

住在芝加哥的人

是不是都會因為 " 仰望 " 而充滿夢想 ???

2002.7.9

今天搬進了新家

除了家具…真的是空無一物呢

我要開始 2 個月一個人住的生活了

嗯…要獨立 !!

今天終於見到了李文雄老師

老師看來很親切啊

2002.7.6

美國的東西好貴，隨便吃一餐都要 7 塊以上

今天起開始自己下廚…

哈哈…第一次就把高麗菜炒焦了… :p

扁扁說我不肯放蒜頭真是怪透了呀

2002.7.12

傍晚，在路旁的草地之上

約莫膝蓋的高度

我看到了一明一滅的綠色光芒

啊 ~~ 霎時超感動的啊

這是我第一次看到綠色光芒的螢火蟲

我要把這些螢火蟲 .. 連同他們散出的火光 ..

輕輕地 ... 收在心裡

然後，一輩子記得這樣的感動

2002.7.13

去了 Lincoln Park Zoo

看到好多好多企鵝喔

不過我希望有一天

我能在野地上看到他們

而非…動物園…

2002.7.18

持續念 paper

哇…怎麼都看不懂… ^^||

2002.7.23

就台灣時間來說…今天，我生日

在 bbs 上，接到了好多 來自好友的祝福

扁扁還趁我不注意的時候

偷偷跑去 starbucks買了小蛋糕回來

喔喔喔… . 好感動啊

原本以為…今年的生日…要寂寞地過了

2002.8.4

終於 .. 開始作實驗了

但我對著 6000 多組數據

坐在電腦前…完全不知如何是好

體會了…書到用時方恨少… >_<

2002.8.15

猶豫了好久 ..

終於下定決心買了那件貴達 50元、印著 U of C 的外套

敗家…但我總覺得要留下些什麼可以做紀念的東西

2002.8.22

今天 meeting ，是我跟扁扁報ㄝ

要用英文講…好緊張

還好大家都說我們報的很好

我想…大家可真是好人啊 ~~

( 我覺得自己報得亂七八糟的 )

2002.8.23

在 U of C 的最後一天

抱著書跑去找老師簽名… .

我在心裡說…

See you, Chicago!!!

2002.8.24

抵達 New York

凌亂的建築

神色匆匆的人群

這是個…不同於 Chicago 的城市

2002.8.28

飛到了 San Francisco

見到了好久不見的大雄

呵呵…大雄也沒變嘛 ~~

2002.8.30

Dear Taiwan, I’m back!! ^^

The EndThe End

Thank you!!!