M*P
发帖数: 6456 | 1 this is very common. if your TF is stress related, you probably have better
chance to see more genes show higher changes. You can check all the
predicted targets of this TF and see whether there is a systematic
differences between these putative target genes, since most of those target
genes may not show significantly changes if you look at them one by one. |
|
T********g
发帖数: 505 | 2 I have three lists of genes, the number of identity of genes are not exactly
same in each list. And each gene has it's own expresion value or
relationship. I would like to know which two lists with expression values
are closer or more similar. How can I get the answer? Which bioinformatic
tool can I use? Thanks. |
|
h***e
发帖数: 232 | 3 Just wondering if there is a way to quantify a specific gene expression in
mixed population of cells.
For example:
Each sample has x number of cells from normal tissue mixed with y number of
cancer cells. x and y are unknown.
How to compare some specific gene expression profiles (those genes only
expressed in cancer cells) among different
samples.
Any reference? |
|
G***G
发帖数: 16778 | 4 where to find all exons/introns for a gene?
I am looking for informations about exons/introns for a gene,
not for one of its transcripts.
For example, given a gene, can we tell how many exons it has totally?
What is exon1 and what is exon2? |
|
t**l
发帖数: 109 | 5 我现在想研究一个gene是否和CCCTC-Binding Factor 有关系。
我想知道这个CTCF的consensus sequence: CCGCGNGGNGGCAG 时候存在我想研究的这个
gene的上下游和内含子中。我应该怎么入手，从来没做个bioinfo方面的工作。还有就
是想biochemially 证明这个CTCF可以结合到这个gene的DNA，但是我不知道哪个地方，
要是做CHIP,怎么选primer呢，总不能一上来就chip-seq， |
|
M********r
发帖数: 142 | 6 太感谢了。FDR过滤后的做，为什么不可以？
还一个问题。我经常遇到1001 error，就是None of the gene sets that you
specified passed the size threshold.
我同事说可能是下载用来比较用的别人的gene set里面包含的基因太少。但是我看了一
下，里面有200多个基因。
也不是 gene identifiers 没设置对，我试了false和ture，都不行。
这是怎么回事？
能设置Min/Max size parameter吗？该怎么设置？
谢谢！！ |
|
c*********r
发帖数: 1312 | 7 推荐手边看过的两篇文献，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
如果只是简单做做，你的gene ID又可以被Gene Ontology Consortium网站默认识别，
直接到
http://geneontology.org/
复制粘贴，选好species，submit就好了。 |
|
|
发帖数: 1 | 9 easy。
不需要会代码。
Google gene ontology加上关键词 g:profiler 或者 gorilla 或者 DAVID 或者
Metascape。把你的基因放进去就行。
如果想同时考虑基因的表达情况，可以用Broad Institute的GSEA，也是用户友好软件
，不需要写代码。这个可以考虑基因的表达高低，比如TPM或者fold change，需要发表
过的reference gene datasets，Broad网站提供各种下载，你读读手册就会用。
[在 vicillibra (vicillibra) 的大作中提到：]
:通过测序手段获得的一堆上调或者下降的基因(excel)
:如何对其进行Gene Ontology/Function Annotation 分析
:筛选到和该疾病相关的基因，从而进行下游分析？
:没有编码经验，求指导，谢谢 |
|
S******y
发帖数: 1123 | 10 I am new to Gene Expression problem. But I am very interested in the
field.
But is Gene Expression problem (most of time) equivalent to variable
selection problem?
Have the following methods been widely used in Gene Expression problem?
- SSVS (Stochastic search variable selection)
- LASSO
- Stepwise
Thanks! |
|
p****r
发帖数: 104 | 11 http://www.biomedcentral.com/1471-2105/9/395
记得2004年的时候，Cell上有一篇很有名的文章：Predicting gene expression from
sequence
作者用了一个Bayesian network从DNA sequence来predict gene expression，号称
accuracy可
以达到80%，引起了轰动。但是文章发表之后，很多人却发现结果无法重复，引起了很
多的争论。
后来就是这几个UCSD的researcher对当初这篇文章进行了仔细的复制，并且改进了方法
，看起来经过改进
之后，这个方法的结果还是不错的。
我想在motif finding之后，一个很自然的延伸就是预测motif之间的关系，并且寻找他
们和gene
expression的联系。这篇文章很好的解答了这个问题。推荐阅读！ |
|
m******1
发帖数: 19713 | 12 By Andi Alexander
Female woman symbol gender x390 (fair) | Advocate.com
Gay men are more likely than lesbians to show gender-nonconforming traits
during childhood, according to a new study by Queen Mary University in
London.
Research following children to adulthood shows that 50%-80% of gender-
nonconforming boys grow up to be gay. Meanwhile, only about one-third of
nonconforming girls become lesbians.
Psychologists Andrea Burri and Qazi Rahman report that genes may be
partially responsible for... 阅读全帖 |
|
l****z
发帖数: 29846 | 13 http://www.breitbart.com/big-hollywood/2016/03/31/gene-simmons-
Rock legend Gene Simmons says that tens of millions of Americans—perhaps as
many as 100 million people—secretly support GOP frontrunner Donald Trump’
s plan to build a wall on the country’s southern border.
During a brief interview with Rolling Stone that was published on Wednesday
Mar. 30, the Kiss frontman opened up about Trump, who he hailed as “the
truest political animal I’ve ever seen onstage.”
“He has no speechwriters, no edi... 阅读全帖 |
|
S*********g
发帖数: 24893 | 14 【 以下文字转载自 Stock 讨论区 】
发信人: StephenKing (金博士), 信区: Stock
标 题: MCP/S/SIRI/GENE/FNMA/FMCC/ADMD/MDCN/MGON/BRCD
发信站: BBS 未名空间站 (Fri Mar 27 23:05:52 2015, 美东)
MCP/S/SIRI/GENE/FNMA/FMCC/ADMD/MDCN/MGON/BRCD
走的都跟我想的不一样
你个猪狗不如的畜生！ |
|
l********n
发帖数: 260 | 15 【 以下文字转载自 Biology 讨论区 】
发信人: liujiatian (liujiatian), 信区: Biology
标 题: Genes and Immunity的版费问题
发信站: BBS 未名空间站 (Fri Jan 25 01:08:50 2013, 美东)
板上有人知道一个杂志genes and immunity吗?
在这个杂志上发表文章的时候到底需要多少版费呢?谢谢 |
|
发帖数: 1 | 16 【 以下文字转载自 Postdoc 讨论区 】
发信人: tonytonyvan (), 信区: Postdoc
标 题: 实验求助：gene rescue
发信站: BBS 未名空间站 (Tue Aug 16 21:13:59 2016, 美东)
最近在做gene rescue，试了一次了，不太成功，但不知道问题出在哪里？不知道哪位
大师做过，请指点。 |
|
l********n
发帖数: 260 | 17 【 以下文字转载自 Biology 讨论区 】
发信人: liujiatian (liujiatian), 信区: Biology
标 题: Genes and Immunity的版费问题
发信站: BBS 未名空间站 (Fri Jan 25 01:08:50 2013, 美东)
板上有人知道一个杂志genes and immunity吗?
在这个杂志上发表文章的时候到底需要多少版费呢?谢谢 |
|
p*****p
发帖数: 61 | 18 【 以下文字转载自 Biology 讨论区 】
发信人: pharlap (梦), 信区: Biology
标 题: 求审稿机会(生物)－－genomics, gene expression regulation, molecular biology
发信站: BBS 未名空间站 (Sat May 19 14:40:34 2012, 美东)
生物博士后，准备申请绿卡，需要积累审稿数量。
尝试给杂志编辑写了几封信没有回音，双管其下，也到这里来寻求帮助
领域关键词：
genomics,medical genomics,gene expression regulation, molecular biology,NGS
data analysis
希望得到推荐
有意帮忙者站内信件联系
非常感谢 |
|
|
d*****r
发帖数: 41 | 20 【 以下文字转载自 LosAngeles 讨论区 】
发信人: danxinr (丹心), 信区: LosAngeles
标 题: UCLA校长Gene Block关于支持SCA5和反对prop209的“雄文”
发信站: BBS 未名空间站 (Thu Mar 13 14:33:15 2014, 美东)
文章来自其本人的主页：
http://chancellor.ucla.edu/updates/the-impact-of-proposition-20
内中提到“The offensive flyer sent to our Asian American Studies Center”，
这里不知何指。难道亚裔会给亚裔的学习中心写offensive flyer？
以下全文：
The Impact of Proposition 209 and Our Duty to Our Students
Chancellor Block calls on UCLA faculty to re-examine the creation of an
undergraduate general ... 阅读全帖 |
|
B*****e
发帖数: 9375 | 21 职业橄榄球球员工会（NFLPA）的执行官Gene Upshaw因胰腺癌今天去世了。
那是最难发现也根本无法治的一种癌症, 他的病情是上个星期刚刚才诊断出来的。
他在NFLPA二十五年, 经历三个NFL总裁, 权力和影响力也可以与他们平起平坐。
球员们在他的领导下, 尽管最近二十年的荣华富贵, 都没有罢工，
而NFL球队的收入, 球员的收入, 和其他的待遇也有极大的改善。
但他却被短视无知的人认定为被招安了的工贼, 内奸，
甚至被同类的Bryant Gumbel公开影射为奴隶, 实在是很不公平的。
现在没有了他, NFL又到了谈判下一个劳资合同的时候,
不知道是否还能谈下来, 或其中很多对NFL整体有利的条款是否还能保留。
以这个系列的文字纪念他。
*** 球员生涯 ***
Gene Upshaw在走上仕途之前在NFL打了15年, 全是为Oakland Raiders效力 |
|
a***a
发帖数: 40617 | 22 【 以下文字转载自 Fitness 讨论区 】
发信人: anoia (high estrogen man), 信区: Fitness
标 题: 这帮货都没后天workout，就是纯gene区别
发信站: BBS 未名空间站 (Tue Jul 24 15:15:58 2012, 美东)
myostatin gene mutation
dogs
cows
mice |
|
a***a
发帖数: 40617 | 23 所以要清楚认识自己的gene limit，放弃不切实际的幻想
另一方面，reasonable的瘦（比如男bodyfat per 15%，女20%）这些都是可以努力
达到的
ripped的瘦，真的只能靠gene，或者你努力也能达到，但是需要太多的effort
得不偿失
同样，瘦了还想有屁股有胸。。。我就不说了。。。 |
|
A******e
发帖数: 3373 | 24 这个东西，你怎么能知道“自己的gene limit”？一般人锻炼又怎么能确定自己是训练
方法问题还是gene的limit问题？
至于得不偿失就更说不清了。你有怎么知道别人付出了巨大的牺牲得的是啥？说不定只
是一句you look good，也说不定就凭着好那么一点点的身材找到了life soul mate。 |
|
H*****r
发帖数: 764 | 25 This isn’t over. This isn’t the one moment, the one stance, that lifts
the Ohio State football program -- the Ohio State University -- out of the
muck and mire.
There are two left, and they’re just around the corner: once athletic
director Gene Smith and president Gordon Gee are fired, the healing and the
rebuilding can begin.
Jim Tressel resigned as coach at Ohio State on Monday, and the first step
has been taken to end this 13-month ordeal of lies, denials and coverups
that threatens to bring ... 阅读全帖 |
|
l***i
发帖数: 167 | 26 our greatest beloved comrade, the chief engineer of mit bbs, Mr. lwzhi
anounced today that, he discovered a gene that cause people to water a lot
in bbs.
if u r too busy to water and want to remove the specific gene, pls contact
with him and turn in $75 unwaivable application fee.
hoho |
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w***e
发帖数: 269 | 27 No, you can't. The expression of gene of interest has to be compared against
that of house-keeping genes. |
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w***d
发帖数: 31 | 28 in theory, it is really painful to compare different genes transcript
expression level by qPCR. you have to go down to the "absolute" number of
transcript. in this situation, relative fold doesn't work. you have to make
known copy number of genes as standard. even after that, you can't be sure
that in your system that PCR efficiency for different sets of primers would
behave the same.
I would say if your difference is kind of dramatic (in relative method), you
would be confident to show the diff |
|
X***n
发帖数: 366 | 29 how about using pKD46 to flank the gene you want to knock out with FRT,then
insert FLP gene downstream the promoter that activate at the specific time
point?
I don't know details :) |
|
i******g
发帖数: 90 | 30 Does anyone know where to buy E. coli gene library (all 4000 genes are
higtagged)? thanks. |
|
B********6
发帖数: 43 | 31 用的是C. elegans
开始我是在NCBI 上找的，给的pqn-46 gene's sequence 是 complement 6941825-
6944674. 可是因为有个字：complement, 我就不知道该如何算pqn-46's promoter
sequence的长度了。pqn-46's upstream gene is F57B9.3, from 6940113-6941672.
请懂得大侠相助，有包子答谢！ |
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x*********a
发帖数: 906 | 32 E. coli host genotype has to be lamda+?
lamda- strains can not express T7 promoter-direced gene from plasmid?
Any other prophage on E. coli K12 has T7 RNA polymerase?
How about SP6 promoter? what kind of genotype can not express SP6 promoter ?
Can this genotype E. coli K12 ∆(araD-araB)567, ∆lacZ4787(::rrnB-
3), lambda-, rph-1, ∆(rhaD-rhaB)568, hsdR514 express SP6 or T7
promoter-driven gene?
Thanks a lot. |
|
x********8
发帖数: 38 | 33 I want to clone a promoter of a mouse gene, so the DNA sequence and the
sequence before the ATG should be find out for primer design.
1. How to search a mouse gene sequence?
2. What database should be use?
3. Any suggestions?
Thanks in advance for your reply. |
|
H****N
发帖数: 997 | 34 Go to http://genome.ucsc.edu/cgi-bin/hgGateway
Search your gene
Click on your gene name to get to the genome browser interface
Click on the referseq link
At links to sequence, click Genomic Sequence from assembly
Specify the length of sequence you want to retrieve and other parameters
You get you sequence |
|
W*****o
发帖数: 1780 | 35 I am annotating genes from a genome. Please help recommend a gene prediction
/scan software. Thanks a lot. |
|
r****q
发帖数: 22 | 36
I can’t agree with you at all on the performance validation. To be concise,
I followed the standard paradigm used in the community. You may only want
to challenge this, when (1) you prove concretely that this paradigm is wrong
; (2) you do not use this one in your own research. Your example on ‘RB1
related with RB’ is misleading and improper. One thing is sure here, a good
method has to be consistent, an inconsistent method is never a good method.
We can argue on this for days. But GAGE has bee... 阅读全帖 |
|
f********n
发帖数: 6465 | 37 make the alignments of your gene sequence with the gene sequences whose
promoter have been clarified. |
|
o**i
发帖数: 1165 | 38 假如gene promoter附近 一点histone modification都没有
这样的gene是不是默认是silent的? |
|
s******y
发帖数: 220 | 39 看到文献里面一般检测hypertrophy的supporting evidence 是检测mRNA水平的fetal
gene marker水平 (ANP,BNP,ACTA1,bMHC)，用northern 或者realtime PCR。
但是没见到用western 检测这些gene在蛋白水平的表达， 请问这是为什么呢？
如果是抗体贵，那grant proposal时候要propose Western blot 吗？
多谢。 |
|
l******o
发帖数: 3764 | 40 那个，如果这个问题比较弱智的话还请不吝赐教 别嘲笑俺：
今天老板让我整理以前实验室genotyping的结果 特别嘱咐让把那些SNP的rs号都写上。
有好几个SNP都是ABO gene的，但是前面的人没有写rs号，就叫它们G703A, G526C这样
的名字。这个G703A，我看了一下，应该就是最常见的A->B吧，但是不知道是不是因为
太常见了，查到的paper都管它叫G703A, 没找到谁用rs编号的
我不太熟悉genetics，最后实在没辙，只好去NCBI上找了ABO gene出来，然后估摸着
extrone上差不多是700的位置放大了，终于看到703上那个SNP叫啥
请问有没有更简单一点的办法呢？ |
|
j********r
发帖数: 156 | 41 最近一直在尝试overexpress a gene in primary epithelial cells, but always
failed to get decent level of expression。望版上诸位帮看一下。
我用的是一个类似与pBabe的retroviral vector, the gene was tagged with GFP or
Flag on the c-terminal. The target cells were infected twice and then
subjected to antibiotic selection (blasticidin in this case). 用anti-
Flag做western, 勉强能看到带，如果用the ab against itself, 可以看到exogenous和
endogeneous的差不多 （the endogenous level is already very low, which is
also the reason that we hope to increase it to ... 阅读全帖 |
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f****h
发帖数: 41 | 42 我联系了DNA2.0和Geneart，我的gene是850bp，DNA2.0要$700，Geneart 要$400多. 怎
么差这么多？如果DNA2.0
贵这么多，还有很多生意，那他们是不是最好的？这是第一次，以后要更多，所以想找
个好点的公司。
gene |
|
e*****t
发帖数: 642 | 43 really? i search some literature. only couples of paper talk about the model
of integration of these three.many ppl do model correlation between cnv and
gene expression or methylation and gene expression. but only few try to put
the three together. there are some statistical issues hard to handle. |
|
W*****o
发帖数: 1780 | 44 I found a new family of genes, which are very different from orthologs in
other species. They do not have introns. What is advantage and disadvantage
of intronless genes? Thanks a lot. |
|
k*****s
发帖数: 36 | 45 Please help!
Is there any company or gene bank from which I can buy/get bacterial gene in
plasmids?
Thanks! |
|
s**x
发帖数: 138 | 46 i tried. i could download text files and read them with excel. the problem
is i could not get the files. i only got 20 genes. i want the complete genes
' expression level in a single file. please tell me how to do. thanks |
|
C*******e
发帖数: 4348 | 47 你这第二步的PCR产物大小对么？
如果promoter和gene之间你没有留overlapping region的话
不太能理解为什么这二步PCR应该work
“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” |
|
C*******e
发帖数: 4348 | 48 promoter reverse和gene forward吧
10bp overlap是不是有点太短了
相对于你两个片段来说（一个1.5kb一个3kb)
这个第二步PCR应该算是mega PCR吧
一般要摸条件优化的
很多时候前5个循环是不放promoter fwd primer和gene reverse primer的
等前几个循环产生足够多的full length template以后
再放两端的primer进去
如果第二步PCR你都不能确定有你要的终产物的话
做TA cloning出不来不奇怪啊
如果你确定有终产物的话
我建议是胶回收以后再做TA cloning
不然乱七八糟东西太多了 |
|
s******y
发帖数: 424 | 49 我没有什么molecular biology 的背景，希望想请教一下。
我通过mass spec可以sequence出来novel peptide，但我怎么查相应的gene里能不能
encode出来这段peptide呢？是不是应该用ncbi的blast protein，但查出来的number 好像是protein 的啊？blast neucleotide查出来的是不是就是gene的accession #了啊 |
|
l**********1
发帖数: 5204 | 50 SNHG5 Prostate cancer ribosome biogenesis
//www.ncbi.nlm.nih.gov/pubmed/19239895
//atlasgeneticsoncology.org/Genes/GC_SNHG5.html
//www.ebi.ac.uk/gxa/gene/ENSG00000203875 |
|
