E******T
发帖数: 59 | 1 Gene module在生物医学癌症分类（clustering），以及生物活性marker鉴定的应用
生物医学样品的分类（clustering）及其复杂，有几个原因： 医学样品的构成，比如
说白血病病人，有年龄，性别，癌症分级（I，II，III），用药情况，癌症类别（AML
，ALL）等等。按照不同的标准，就可以把病人样品分成不同的类别（clustering）.
更深一层次，不同的类别如果从生物学上来看，是由不同的基因，信号通路引起。如果
能找到这些不同类别对应的pathway,那么相对应的分类也就能被发现。 比如，白血病
里面的一种AML，他相应的信号通路就不同于另一种ALL，所以根据这些基因就能把白血
病分成AML和ALL。同理，如果能发现与癌症分级不同的信号通路，就能把白血病分成I
，II，III等不同的级别。但是，在平常的研究当中，这些具体的分类都不是特别清楚
。大多数情况下，仅仅知道其中的一种，比如在白血病里面就知道AML和ALL的分类，至
于其他的信息，很难得到。所以我们用了unsupervised learning的思想来研究这个问
题。
从生物角度来看，如果一个pat... 阅读全帖 |
|
r**********e
发帖数: 587 | 2 要研究某一种transposon element在基因组的分布情况。就是根据repeatmasker，
找出所有含有at least one such transposon element的基因，然后把gene list直接
放到GO term里去（这里background gene set就是default的人类基因组的所有基因）
。目的是看这些基因是否专门富集到某种category
最后结果的top hit是channel gene；但是有一个问题，很多channel gene（或者广义
说brain gene）整个的gene size就比一般的基因大的多，有非常长的intron区域。
对于gene enrichment/ontology,这个基因长度是不是很大的bias？我搜索到一些paper
也有讨论这个问题的。我不知道gene ontology的网站或者什么DAVID在计算的时候是否
已经考虑了这个基因大小的bias？
我还有一个想法，就是那gene size作为分母，而一个基因里含有几个transposon
element作为分子；这样一除就是一个权重score，比如：
g... 阅读全帖 |
|
发帖数: 1 | 3 转自Bloomberg：
https://www.bloomberg.com/amp/opinion/articles/2018-11-27/crispr-fears-
designer-baby-outrage-won-t-last-as-ethics-evolve
It’s too soon to know whether a Chinese researcher who claims to have
successfully edited the genomes of newly born twins is telling the truth.
But if he is, and if the girls turn out to be healthy and normal, it heralds
a significant change in the scientific and ethical status of human gene
editing. The outrage might not last long.
The consensus in the scientifi... 阅读全帖 |
|
A*******y
发帖数: 11148 | 4 A large international consortium of researchers has produced the first
comprehensive, detailed map of the way genes work across the major cells and
tissues of the human body. The findings describe the complex networks that
govern gene activity, and the new information could play a crucial role in
identifying the genes involved with disease.
"Now, for the first time, we are able to pinpoint the regions of the genome
that can be active in a disease and in normal activity, whether it's in a
brain c... 阅读全帖 |
|
c*********r
发帖数: 1312 | 5 你做DE analysis的时候是用什么package？
如果是DESeq2或者EdgeR，默认不需要考虑gene length。因为默认是比较相对表达变化
，不依赖于gene length。control和treatment或者不同tissue的reference都是一样的
，gene length也都是一样的，所以不依赖于gene length。除非你用不同的reference。
然后GO analysis input 是DE analysis output，只分析那些DE gene，也和gene
length无关。
写到这里我又看了一下你的问题，突然明白了我以上回答答非所问。。。
你只看了某“一个”TF的binding site，然后把这一个list，没有做任何DE，直接放到
GO里了吗？如果只有一个组织，没有做DE，我不确定这样做是否正确。
如果是同一个TF，但是有两个或更多的不同组织，做了DE之后，然后把DE list放到GO
里，应该没问题，也不需要考虑gene length。理由同上。 |
|
j******i
发帖数: 939 | 6 LZ做genetherapy的吗 终于碰到同行了
纯genetherapy的杂志不多 主要是human gene therapy, gene therapy, 然后是cancer
gene therapy等一些特定领域的gene therapy. molecular therapy影响因子是里边最
高的。gene therapy的大牛在上边都有文章。要想在gene therapy领域混，怎么也要在
molecular therapy上混个脸熟哈。 |
|
r**********e
发帖数: 587 | 7 我就是先MACS算出所有的peaks，bed format，chr:start-end
然后根据这个bed去intersect hg19 gene list
这样就得到所有至少含有一个peaks的gene的list
我的目的就是想看看至少含有一个peaks的gene到底是什么category的(但就会有gene
length bias这个问题)
“考虑过gene length之后算出来的一个list”
怎么算呢？如我说的，比如gene A，这个基因里有3个binding sites，然后基因长度是
10000，然后3/10000就是这个geneA的权重score？
然后人为的设置一个cutoff？比如score排名top 100的基因筛选出来进行 GO TERM? |
|
G***G
发帖数: 16778 | 8 from DNA-Seq, a mutation happens in gene BRAF.
what should we do in RNA-SEQ?
1) detect gene BRAF
2) detect mutated gene BRAF.
if we do the second, what do we need?
1) normal transcript file
2) customized transcript file for mutated gene BRAF.
if we use 1, we can identify the gene BRAF, but can we say we find mutated
gene BRAF? |
|
k******e
发帖数: 8870 | 9 here is an example for gene therapy in JCR.
1.Search for a specific journal
2. input: gene therapy
3.click: GENE THER
4. find that GENE THER is belongs to: "Subject Categories:
BIOCHEMISTRY & MOLECULAR BIOLOGY"
5. go back to JCR
6. "View a group of journals by Subject Category"
7. select: BIOCHEMISTRY & MOLECULAR BIOLOGY
8. select sort by different way. for IF, gene ther ranks 67 out of 286
journals in BIOCHEMISTRY & MOLECULAR BIOLOGY |
|
|
w*****s
发帖数: 122 | 11 April 11, 2000] Gene Expression Markup Language (GEML). A communiqufrom Michael
Hoffman of Rosetta Inpharmatics reports on the development of GEML - an open-standard XML format
for DNA microarray and gene expression data. The Gene Expression Markup Language (GEML) "is a file
format for storing DNA microarray and gene expression data for chip patterns and chip scans (profiles).
GEML is an open-standard XML format which enables exchanging data between a variety of gene
expressi |
|
t****p
发帖数: 1504 | 12 For example, if you randomly put insert into genome and cover/saturate all
of genes, therefore create a large mutant strains library. How to find these
essential genes?
If there is no any insert in a gene coding region from this mutant library,
we would say this is an essential gene. But how about all of insertions
happen at very c-terminal of the coding region? Would you still call this
essential gene? What is the standard? |
|
g*********d
发帖数: 233 | 13 Here is some literature I found....
I'm interested in this gene
Thanks!
2'-5'-oligoadenylate synthetase 1 is an enzyme that in humans is encoded
by the OAS1 gene.[1][2]
This gene encodes a member of the 2-5A synthetase family, essential
proteins involved in the innate immune response to viral infection. The
encoded protein is induced by interferons and uses adenosine triphosphate
in 2'-specific nucleotidyl transfer reactions to synthesize 2',5'-
oligoadenylates (2-5As). These molecules activate ... 阅读全帖 |
|
O*********e
发帖数: 79 | 14 我一般用两到三个housekeeping gene，比如actin, GAPDH，做qRT-PCR的internal
control。分析数据的时候，我分别用这几个gene来计算我的experimental genes的
fold change，然后取平均值得到最终结果。今天在网上找到一个分析qRT-PCR结果的
Excel模板，它里面的计算方法是，先把housekeeping gene的Ct value取平均值，再用
这个平均值来计算experimental genes的fold change。这两种方法最后得到的结果是
一致的吗？这貌似是个数学问题，而我每每遇到数学就头晕，所以上来问问大家的看法
，还有大家平时都用的哪种算法？先谢谢了！ |
|
r*s
发帖数: 2555 | 15 FDA approves first gene therapy in U.S. to treat leukemia
Last Updated Aug 30, 2017 7:37 PM EDT
WASHINGTON -- Opening a new era in cancer care, the Food and Drug
Administration on Wednesday approved the first treatment that genetically
engineers patients' own blood cells into an army of assassins to seek and
destroy childhood leukemia.
The CAR-T cell treatment developed by Novartis and the University of
Pennsylvania is the first type of gene therapy to hit the U.S. market — and
one in a powerf... 阅读全帖 |
|
w********h
发帖数: 12367 | 16 Polymers are promising tools for gene therapy
April 24, 2002 - New methods are being developed to cure illnesses with the
aid of gene therapy. Polymer technology provides new and versatile
possibilities for administering gene doses.
"?Polymers are used to pack the gene to be transferred into particles of the
size of a ten thousandth of a millimetre. These polymers effectively
transport the transferable gene into affected cells and are then dissolved
by the organs,"? explains Project Coordinator, |
|
y****t
发帖数: 10233 | 17 继科学家们发现小左们的脑残基因DRD4后,发现此基也是slut gene.
"What we found was that individuals with a certain variant of the DRD4 gene
were more likely to have a history of uncommitted sex, including one-night
stands and infidelity,"
http://news.yahoo.com/s/time/20101202/hl_time/httphealthlandtimecom20101202toomanyonenightstandsblameyourgenesxidrssfullhealthsciyahoo
一切都很make sense.
我老人家虽然不是所谓的科学家,但我老可以用common sense预言,
科学终将会证明,这个基因的存在与影
响跟年纪大小有关,并跟小孩早期的洗脑教育也有很深的关系.大多数人,随着年龄的增
长,此基因会趋稳,而少数被洗脑太深,或药物作用太厉害(e.g. pot heads... 阅读全帖 |
|
g********s
发帖数: 3652 | 18 借SCA5的机会，这个 Gene Block 放出来了！网友揭露他说：
-- 我Suffer了很多年了
-- 我看着这么多亚裔不爽
-- 中国人 horrible
他这就是种族歧视，为什么我们听之任之？他身在高位，这个影响多么恶劣？
请把以上的链接放在这里，我们请三个华人议员戴罪立功，让他们写公开信给UC的管理
层要求开除Gene Block ！
如果我们不收拾一个猖獗的Gene Block ，所有Gene Block就会肆无忌惮地，用各种手
段欺负我们的孩子！ |
|
z**t
发帖数: 83 | 19 "Gene Roddenberry's Andromeda is a weekly syndicated science-fiction action
hour. The concept was developed by Robert Hewitt Wolfe (who worked on Star
Trek: Deep Space Nine) using unpublished notes that Gene Roddenberry's widow
provided from his personal papers. Using some consistent philosophies and
themes in Gene Roddenberry's work to provide stories and characters, the
universe of Andromeda was born.
It is a completely different universe from any of Gene Roddenberry's other
creations. They do |
|
s****6
发帖数: 34 | 20 Thank you very much for this wonderful sharing. While what you said is very
valuable and I appreciate it, I was asking about how to deal with those
undefined or uncharacterized genes, like those we met when we used the Affy
HG-U133_plus 2 chips. Some of the probes are from EST and unknow genes. I
got a few of them significantly changed in my treatment. Is it worthwhile to
pursue those "genes" for the sake of novelty? If yes, how to proceed? Do I
have a burden to prove these are truely some gene |
|
r****q
发帖数: 22 | 21 If you know R/Bioconductor, you may want to try GAGE. No need to remove
genes or discriminate genes with or without annotation. Different from
hypergeometric test based methods/programs like DAVID, GAGE uses all genes
and requires no pre-selection of differentially expressed (or otherwise
significant) gene list. This strategy frequently leads to more robust and
sensitive analysis results.
The gage package is available with Bioconductor at:
http://bioconductor.org/help/bioc-views/release/bioc/htm... 阅读全帖 |
|
r****q
发帖数: 22 | 22 ‘RB1 is related to RB’ is a statement, not a prediction or inference. You
may develop this into a problem to solve, but it is nothing more than a
meaningless or trivial one. I don’t see any comparability between solving
this problem and gene set analysis.
I never say experiment evidence is not needed. I just say it was not needed
to do our own verification experiment there. GAGE identified so many
pathways that GSEA and PAGE did not, and whose biological relevance has been
well established in li... 阅读全帖 |
|
i*********0
发帖数: 915 | 23 我做的gene (A)在胚胎早期deletion导致lethal phenotype,我想看看在胚胎发育中期
或者晚期 (从15.5开始)deletion, A
gene 对发育的影响. 我的一个line的老鼠是A gene flox/flox, ER-cre+ 的,我想用
OHT 或者4-OHT 在E15.5的时候诱导
A gene deletion, 目前考虑两种方法:一是做ip注射好,二是是通过drinking water.
我只看过一些在成体做Ip 的paper,但是
用的volume都比较大,我也不想给怀孕老鼠更多的stress. drinking water倒是没有伤
害,但是我担心deletion的效率不高.
不知道那位有更好的办法,或者comment一下我列举的.
谢谢! |
|
u****w
发帖数: 21 | 24 请问各位牛人如何查gene A与gene B是否在转录水平相互条件或者单方面调节？pubmed
目前还没这
两gene同时的paper，但如何断定有转录上的关联嘞？多谢多谢 |
|
r******y
发帖数: 21907 | 25 我现在需要把promoter和gene CDS克隆到一起。我先是分别克隆promoter and gene
CDS，然后pcr clean-up后把两者混合起来再分别用promoter的forward primer + gene
reverse primer做pcr，可是TA cloning后总不对，跑胶后看到合适大小的带也很弱，
我的pcr混合产物作了1:10 dilution。gene CDS is around 3.5 kb, promoter is 1.5
kb.是不是太长了？请指教！如果用gDNA序列太大了，以后也不好做。。。-- |
|
j****x
发帖数: 1704 | 26 呵呵，所谓single copy gene自然是针对单倍体基因组而言了吧，否则注释gene locus
的时候不是得标两个chromesome，两个start/end bp，啥都得双份啦
house keeping gene是不是很多都有duplication/gene family，或者pseudogene什么
，希望能避免这些相似序列对PCR的影响。
谢谢！ |
|
a******a
发帖数: 283 | 27 We want to detect a gene of interest inserted into human genome by
retrovirus, using qPCR. That said human genome will be in the background and
the gene of interest should have no overlap with human genome. However the
gene of interest is high GC content (around 70%). Currently we are building
a standard curve by mocking the reaction condition, but the result is not
that well.
Any recommendation? Anybody familiar with detecting gene insert in the
genome? Any recommendation regarding good literat... 阅读全帖 |
|
G***G
发帖数: 16778 | 28 two genes are from a to b in the same chromosome.
But one is from positive strand.
another is from negative strand.
What is relationship between the two genes?
Are they actually one gene or two different genes? |
|
i*S
发帖数: 175 | 29 好吧我又回来了……对生物信息一窍不通啊。 上次求助谢谢好心的朋友，不过我自己
手动“生物”信息地解决了……这次一定发包子。
我最近做了质谱，鉴定出了1000多个蛋白，现在想对这些蛋白做一下Gene Ontology的
分析，不知道怎么办才好呢？
我现在有的是这些蛋白的gi number和Uniprot Accession Number，全在Excel的表格里
面。我也找到了分析gene ontology的傻瓜在线工具比如Panther，但是发现它的数据库
好像没有Uniprot每个蛋白单独网页上显示的全：有的蛋白找不到，或者就是有的蛋白
信息不足。而且好像作图也很难看。
我最终的目的是想把这些蛋白根据gene ontology的信息做成饼状图或者是bar graph。
想求助一下大家，对于像我这种对coding没什么经验的，有什么方法能做Gene
Ontology的分析？ 有比Panther更好的工具吗？ 或者有什么方法可以抓取Uniprot上面
的GO信息呢？ 抑或如果学习coding或者sql什么是必要的，有什么针对GO analysis这
方面的入门教程嘛？
多谢了！ |
|
r**********e
发帖数: 587 | 30 请问gene ontology/enrichment的做法
感觉各种gene ontology, pathway enrichment等等的数据库，网站非常多。
不知道最有公信力或者常用的是什么？GO term? DAVID?
如果我的gene enrich只在DAVID里是significant的，而在其他数据库不是，那我就只
show DAVID的结果？show对自己最有利的？这个算cheating吗？
另外，对于adjusted p-value，比如bonferoni，觉得这个过于保守；如果我的结果得
到了比如2*10^(-4)的p-value，但还是没达到bonferoni的水平，可以report吗？
个人感觉gene enrichment分析，太多猫腻，而且很多都是鸡肋凑个图
听听大家的看法 |
|
c*********r
发帖数: 1312 | 31 推荐手边看过的两篇review，有点老，但挺好：
1. Use and misuse of the gene ontology annotations
2. Ten years of pathway analysis: current approaches and outstanding
challenges
我觉得GSEA应该比gene ontology更好一些。Gene Ontology只考虑p value上有显著差
异的那些gene，丢失了表达量等信息。
下游的验证还是更重要。 |
|
R****n
发帖数: 708 | 32 Mark
[在 cellcreator (cellcreator) 的大作中提到：]
:推荐手边看过的两篇review，有点老，但挺好：
:1. Use and misuse of the gene ontology annotations
:challenges
:我觉得GSEA应该比gene ontology更好一些。Gene Ontology只考虑p value上有显著差
:异的那些gene，丢失了表达量等信息。
:下游的验证还是更重要。 |
|
c*********r
发帖数: 1312 | 33 如果是RNA-seq DE之后的GO分析我熟。像你这种的ChIP-seq之后没有做differential
expression（DE）分析的GO分析，我就不太熟悉了。如果是用来比较TFBS的“密度”或
者“浓度”，我觉得需要考虑gene length。但是具体怎么做，我不知道。
如果是做DE之后做GO，毕竟需要一个p-value的cutoff来决定你的gene list。你这种情
况你怎么确定你的gene list的？这个gene list的大小和选择标准直接关系到后面的GO
分析的结果。
one |
|
c*********r
发帖数: 1312 | 34 我也没做过，想想就觉得不容易。RNA-seq大多数基因都有明确的boundary，很好统计
每个gene/transcript的count。但是ChIP-seq就太复杂了。是按照每个binding site在
不同条件下来比较呢？还是调节某个基因的所有binding sites来比较？后者不但要考
虑gene length，还要考虑如何定义哪些binding sites是调节哪个基因的，这个现有知
识估计还不完全吧。
简单查了一下，目前differential binding analysis（我之前叫DE其实不对），几乎
都是比较单个的binding site/peak的count差异（如果是这样的话我觉得应该不用考虑
基因长度的影响）。下边篇文章比较了十几个ChIP-seq differential analysis的软件
，简单的提到了gene ontology，找nearest gene。所以应该还是可以做GO的。里边也
提到length of differential region, 不过我就没有细看了。希望能有点帮助。
http://bib.oxfordjournals.o... 阅读全帖 |
|
w********h
发帖数: 12367 | 35 Development Of New Polymer Delivery Vehicles For Gene Therapy
MIT scientists are reporting synthesis and laboratory tests of a promising
new group of degradable polymer delivery vehicles for gene therapy. The
polymers are improved versions of materials first described in 2000 that
deliver genes efficiently to specific cells.
The lack of a safe, efficient delivery system for DNA has been a major
barrier to clinical use of gene therapy. Viruses and various polymer
materials have been used in effor |
|
w********h
发帖数: 12367 | 36 What's Next For Gene Therapy? Plastics Researchers Design Polymer
Macromolecules As Gene Transfer Agents
Gene therapy depends upon foreign DNA, even viruses, to deliver genes,
therapeutic proteins, or medicine to cells within the body. Many scientists
are looking for better chaperones across the cell membrane. Virginia Tech
researchers think polymer molecules can be created to do the job.
The research will be presented at the 232nd national meeting of the American
Chemical Society in San Francis |
|
w********h
发帖数: 12367 | 37 Polymer Gel Can Block Toxic Leakage Problem in Gene Therapy
Duke engineers identify technique to confine most cell-killing gene products
to targeted tumor
Friday, November 18, 2005
Durham, N.C. -- Duke University biomedical engineers have devised a
potentially patentable method to arrest toxic leakages of genetically
engineered viruses that have plagued attempts to use gene therapy against
cancerous tumors. The problem has been that viruses carrying anti-tumor
genes have tended to leak from tumo |
|
y****t
发帖数: 10233 | 38 【 以下文字转载自 SanFrancisco 讨论区 】
发信人: yourtt (rainmaker), 信区: SanFrancisco
标 题: Scientists Find 'Liberal Gene'
发信站: BBS 未名空间站 (Thu Oct 28 02:18:57 2010, 美东)
According to scientists at UC San Diego and Harvard University, "ideology is
affected not just by social factors, but also by a dopamine receptor gene
called DRD4." That and how many friends you had during high school.
http://www.nbcsandiego.com/news/weird/Scientists-May-Have-IDd-Liberal-Gene-105917218.html
当今的科学界太娱乐了,我又想起了一句老话:
Liberalism is a... 阅读全帖 |
|
B**W
发帖数: 2273 | 39 Genes Play Major Role in Primate Social Behavior, Study Finds
By NICHOLAS WADE
Social behavior among primates — including humans — has a substantial
genetic basis, a team of scientists has concluded from a new survey of
social structure across the primate family tree.
The scientists, at the University of Oxford in England, looked at the
evolutionary family tree of 217 primate species whose social organization is
known. Their findings, published in the journal Nature, challenge some of
the leadin... 阅读全帖 |
|
y****t
发帖数: 10233 | 40 The same gene has already been linked to alcoholism and gambling addiction,
as well as less destructive thrills like a love of horror films. One study
linked the gene to an openness to new social situations, which in turn
correlated with
political liberalism.
http://www.livescience.com/9043-sleep-blame-genes.html |
|
y*****y
发帖数: 3433 | 41 早上去OCC，大门玻璃上贴了一个通知，“Gene Porter的葬礼，中午11点在大厅举行。”
这个跟我当然没什么太大关系，生老病死，时至则行，人不能控制的东西，多想无益。
下午又去，进门的时候在里面的桌子上看到一张葬礼的程序单，看到封面上的照片我愣
住了，这人我知道的。Gene Porter， “The Man” in Dixie’s BBQ.
想起来前年年底我还写过一篇 Dixie's BBQ and THE Man, 那时就知道他得了癌症，那
段饭吃得味同嚼蜡。
程序单上看来的一段话：
He lived hard! A former race car driver, semi pro football player and
just the Man about the town. He is quite the character.
We have truly lost a shining star.
心情挺复杂，年纪越来越大，生老病死也慢慢浮现在地平线上。努力生活，莫留遗憾。
Gene Porter died of cancer on February 28, |
|
l**********n
发帖数: 201 | 42 http://www.nytimes.com/2010/04/27/science/27gene.html
Edward M. Marcotte is looking for drugs that can kill tumors by stopping
blood vessel growth, and he and his colleagues at the University of Texas at
Austin recently found some good targets — five human genes that are
essential for that growth. Now they’re hunting for drugs that can stop
those genes from working. Strangely, though, Dr. Marcotte did not discover
the new genes in the human genome, nor in lab mice or even fruit flies. He
and his |
|
a*****n
发帖数: 2835 | 43 gene trap 做老鼠现在很火啊，直接google gene trap就能找到专门的网站
TIGM现在很多gene trap ES cell lines
了？ |
|
|
r****q
发帖数: 22 | 45 I feel that I am going through one harsh reviwing process with a very
hostile reviwer for publishing my work in mitbbs.
Let’s talk about science first. Yes, 1-on-1 comparison is a key feature of
GAGE. The random fluctuations of TF you mentioned are not rare. But if a big
fluctuation is real random, and you will only see the target gene set
significant in only a small subset of the samples. The global p-value will
remain in-signficant due to the insignificance in other samples. What if
this gene ... 阅读全帖 |
|
o********r
发帖数: 775 | 46 先说你后面的：
：consistency
不试验证明找到的新的发现是真的，而且有biological significance以前，啥都不算
，俺永远predict RB1和RB有关，这个基本上永远没错，而且永远consistent。
：sensitivity/selectivity
By simulation?没用，每个人都可以找到一个model说明自己的方法是世界上最牛的（
别人也可以设计另一个model证明你的东西完全错了）。用俺前老板的话，simulation
只能证明你的方法没用，不能证明有用。
：BIOLOGICAL RELEVANCE.
如果你是通过翻文献或者GO code/IPR之类的，算了，太主观了。比如找到一个set和
Ubiquitin有关，估计啥phenotype都能往上套。想要证明这个东西是对的，唯一的方法
是做试验，比如说你predict某些gene overexpression会引起 metastasis，那就去动
物体内去验证，至少也要在cell line里证实。当然，现在绝大多数bioinfo的文章都是
主观说biologically relevant... 阅读全帖 |
|
o********r
发帖数: 775 | 47 我很理解你不同意我对GAGE的看法，我也没有准备说服你。
关于你说的consistency和biological relevance放一起的说法，嘿嘿，你认为我说的
RB1 gene和RB相关这个论述是缺乏consistency呢还是biological relevance？至于你
说不做实验验证的理由是不需要，这个说法是在让人失望。你说找不到人做实验都比这
个强无数，不需要实验验证说明啥？说明你们找到的所谓consistent and
biologically relevant的东西都是别人找到的。难道你向你的潜在用户推荐的时候说
，我的东西好，找到的东西都不需要实验验证，因为那些都有人发现了。。。话说我自
己用这种方法发文章的时候还是做出了新的预测，并且试图找人实验证实，只是最后未
果。这就是我说的证明你东西的办法：predict一个没有人预测过的东西，然后做实验
去证明。
最后，重申一下，我前面指出的场景是有可能出现的：通过clustering找到了一个co-
regulated set（实际和某TF活性相关），并且可能有biological relevance，自然就
成为一个... 阅读全帖 |
|
d****t
发帖数: 139 | 48 yes, I used SABiosciences online software before. Of course, The Ct of
different HK genes varies big, but as long as it doesn't vary much between
samples for the same gene, it is a good internal control. It has 5 HK genes
on one plate, so you can choose the good ones as your control. |
|
T*****n
发帖数: 274 | 49 其实也要视实际情况。比如knock out target gene的一个exon by introducing
frameshift and stop codon (对于很多很大的基因来说，这样做很常见），如果
RT－PCR的一条引物在敲掉区域，肯定是检测不到mRNA的；但实际上target
gene有可能表达为truncated/mutated form，这样子的话RT-PCR就会出错。
这种情况下，RT-PCR引物扩增没有delete的片段更加可靠,它可以明确告诉你target
gene是否有表达为任何形式。
当然，最可靠的手段还是southern和western。 |
|
L******e
发帖数: 679 | 50 The following experiments were finished:
1: gene expression is increased significantly in tumor compared with the
corresponding normal tissue (RT-PCR for mRNA)
2: Protein expression in tumor cell is significantly increased (western blot)
3: Cell migration assay showed the stimulation in the overexpressing cells.
4; Gene silencing indicated the inhibition of some 'stree', which is related
to the gene.
What else need to do? Is thre a routine rule for the approval of an oncogene?
Thanks. |
|
