发信人: accura (指导,温火焖烧锅), 信区: Biology
标 题: Re: My opinion - Re: DNA microarry bioinformatics?
发信站: The unknown SPACE (Sat May 19 18:59:34 2001), 站内信件

技术发展很难预计的。
不知道你这里microarray和DNA chip有什么区别，指PCR的print
和oligo Array之间的差别么？如果是这样的话，�

microarray较affy chip存在的理由，是PCR product的print并不需要
知道完全的序列，而chip制造的基础在于你需要知道sequence,构建
oligo库，制造芯片。

从数据的角度而言，两者的数据分析都存在着极大的variance, 所以实际
上，现在能利用的数据只是得到的数据的冰山一角而已。看过pat brown的
paper么？不做repeat, 做上上千种条件。对于每一张slide, 数据实际上
没有意义的，但是当把上千张slide cluster到一块的时候，这些数据就变
得有意义了。

从零一个角度而言，从现有的分析中，我们只能关注那些极端express或者
repress的基因，就如你列的那些文章，作为一般实验技术的前导与辅助，
去研究某个具体的基因，具体的条件而已，但这只是microarray/chip运用
的一个方面而已

如何能提高技术的精确度，如何能运用大量不是特别极端的数据，这是
很多statistist和engineer的任务，进而如何通过大量的数据，借助文献和
其他genomic wide的technique的辅助，去构建整个genome的运作，去确定
大量unkown function的gene的功能，而不是简简单单的做个cluster完事
是array-ist和bioinfo-ist的另一个任务。有人给这样的工作取了个名字：
In Silico, 就像in vitro 和 in vivo 一样.


【 在 leohawk (leohawk) 的大作中提到: 】
: I think DNA microarray will SOON be out of date (my personal
: opinion, don't feel offended) -- not the reason mentioned by
: musician, but because I think
: soon the test will be saturated and a more systematic way
: for data analysis will
: emerge, by that time, most microarray facility will find
: nothing to do. Basically, microarray has to be combined with
: other techniques...
: As to success research using DNA chip, there are several
: very good papers out there. One in cell, about a yeast
: expression compendium, which they successfully predicted 7
: orf of previously unknow function. Another in Science, in
: which they studied Gal4 of yeast, showing there are other
: gene that we didn't know before... there is also one for
: studying meiotic recombination hot spots in yeast genome...
: All these researches showed the power of DNA chip. But DNA
: chip will soon become a routine; low-level work, with only a
: few good, mature softwares to analyze the data, which means
: a lot people will lose their job as their product is not
: good enough.
: Take bioinformatics as a whole, the heat will be gone soon,
: after the genome data finished, good algorithm or prediction
: method developed(only by real strong teams), time will come
: where people has to go back to bench work -- only with a
: very good new tool, bioinformatically predicted research
: direction. By then, most nowaday's bioinformatists will find
: hard to keep the job -- personal opinion, welcome any
: comments.
: 【 在 musician (自由心) 的大作中提到: 】
: : The data from the protein array paper is quite crappy/preliminary.
: : Personaly, (maybe a little arrogant), I don't think very highly
: : of gene chip, particularly due to the following reasons.
: : 1. Absolute concentration measurement is almost impossible for gene chips,
: : at least for now.
: : 2. hybridzation techinique is inherently problematic in that inperfect hybri-
: : dization sometimes lights up as well (well, Affy chip does deal with it,
: : but not to a satisfactory level. You can also increase specificity by
: : increasing size of oligos, i guess).
: : 3. I still sincerely doubt the accuracy the data produced from microarray.
: : first, affy admitted errors in their chip 'Affy said they were 'relieved' that their top chip (with the most
: : useful genes) was 'only' 30% wrong...' in recent science journal.
: : Second, so far, I have not seen systematic study on data, i.e, repeat of the same
: : experiment for a few times to see how consistant the data are.


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※ 修改:．accura 于 May 19 19:47:06 修改本文．[FROM: 128.104.113.43]
※ 来源:．The unknown SPACE bbs.mit.edu．[FROM: 128.104.113.43]