a***y
发帖数: 19743 | 1 有一些病人transcriptome的数据
虽然有证据标明我们的样本似乎有一些marker和糖尿病有关，但是我们做的其实完全不
是糖尿病。
所以当分析这些microarray data的时候，一个很长的list，有不同的参数可以重新排
列看那些基因比较重要。
但是很常见的情况是，往往排在最前面的是一些和糖尿病，metabolic syndrome，甚至
癌症有关的基因。
不知道是因为研究肥胖，心脏病，糖尿病的实验多，导致随便找个基因就是类似的
association就出来了，还是真的这些基因在我们研究的问题上也有作用……是不是癌
症糖尿病肥胖研究带来的annotation bias啊？
怎么办啊…… |
l**********1
发帖数: 5204 | 2 pay USDollar 2K per year to KEGG
then dig deeper mining data etc
according to below paper:
//jaguar.biologie.hu-berlin.de/~schaber/papers/Schaber2009IETSB.pdf
its Fig. 2
or this Master dissertation:
//etd.ohiolink.edu/send-pdf.cgi/Ananthanpillai%20Balaji.pdf?ucin1259080814
also please refer below figure:
cited from Book Chapter:
//www.intechopen.com/books/data_mining_and_knowledge_discovery_in_real_life_applications/data_minin
g_in_the_molecular_biology_era_-_a_study_directed_to_carbohydrates_biosynthesis_and_accu
last please go to:
http://www.mitbbs.com/article_t/Biology/31648237.html
3rd floor
NB:
if without their ID from KEGG
please try HUGO and Uniport etc for get all IDs
//www.uniprot.org/help/about
//www.hugo-international.org/index.php
【在 a***y 的大作中提到】
: 有一些病人transcriptome的数据
: 虽然有证据标明我们的样本似乎有一些marker和糖尿病有关，但是我们做的其实完全不
: 是糖尿病。
: 所以当分析这些microarray data的时候，一个很长的list，有不同的参数可以重新排
: 列看那些基因比较重要。
: 但是很常见的情况是，往往排在最前面的是一些和糖尿病，metabolic syndrome，甚至
: 癌症有关的基因。
: 不知道是因为研究肥胖，心脏病，糖尿病的实验多，导致随便找个基因就是类似的
: association就出来了，还是真的这些基因在我们研究的问题上也有作用……是不是癌
: 症糖尿病肥胖研究带来的annotation bias啊？
|
s******a
发帖数: 252 | 3 KEGG is never the best source of transcriptomic analysis.
Pay me $2K, I will give you the analysis in 24 hrs. LOL
But seriously, find some help in stead of wasting time. |
a***y
发帖数: 19743 | 4 啊。
KEGG貌似有用不过不免费了的话我也没经费subscribe啊。
其他的看起来慢复杂的。但是我大概明白了你的意思。
UniProt我再细细研究一下。
life_applications/data_minin
【在 l**********1 的大作中提到】
: pay USDollar 2K per year to KEGG
: then dig deeper mining data etc
: according to below paper:
: //jaguar.biologie.hu-berlin.de/~schaber/papers/Schaber2009IETSB.pdf
: its Fig. 2
: or this Master dissertation:
: //etd.ohiolink.edu/send-pdf.cgi/Ananthanpillai%20Balaji.pdf?ucin1259080814
: also please refer below figure:
: cited from Book Chapter:
: //www.intechopen.com/books/data_mining_and_knowledge_discovery_in_real_life_applications/data_minin
|
a***y
发帖数: 19743 | 5 数据是已经被biostatistician/informatician分析过了
但是接下来就是要make sense那些基因真的有意义，这个貌似别人也没法帮忙
因为课题还是很新的领域，literature search也没有发现有多少相关的研究
扫过这些gene list的时候，很多有微弱证据表明和我最开始提到的疾病有关，所以我
不知道是因为这些annotation是已经biased towards这些疾病，还是真的就是相关。
所以之前lotkaeuler11的意思大概是放到network里面看看，如果我读懂了的话。
参数是有了，可以根据不同的标准进行rank，但是还是只能人工的一个一个的把top
candidate细看才知道有没有价值吧？
【在 s******a 的大作中提到】
: KEGG is never the best source of transcriptomic analysis.
: Pay me $2K, I will give you the analysis in 24 hrs. LOL
: But seriously, find some help in stead of wasting time.
|
a***y
发帖数: 19743 | 6 HUGO上有什么resources，没看到啊
life_applications/data_minin
【在 l**********1 的大作中提到】
: pay USDollar 2K per year to KEGG
: then dig deeper mining data etc
: according to below paper:
: //jaguar.biologie.hu-berlin.de/~schaber/papers/Schaber2009IETSB.pdf
: its Fig. 2
: or this Master dissertation:
: //etd.ohiolink.edu/send-pdf.cgi/Ananthanpillai%20Balaji.pdf?ucin1259080814
: also please refer below figure:
: cited from Book Chapter:
: //www.intechopen.com/books/data_mining_and_knowledge_discovery_in_real_life_applications/data_minin
|
j*p
发帖数: 411 | 7 Try DAVID (there is KEGG pathway) or ingenuity pathway analysis and get your
genelist ranked in someway. Instead of trying them one by one blindly, you
need to kind of having an idea to try which ones first. |
l**********1
发帖数: 5204 | 8 HTTPS//portal.dnb.de/resolver.htm?identifier=988098547&contentkey=34
//www.bioparadigms.org/slc/menu.asp
【在 a***y 的大作中提到】
: HUGO上有什么resources，没看到啊
:
: life_applications/data_minin
|
l**********1
发帖数: 5204 | 9 Bingo
//www.ncbi.nlm.nih.gov/pmc/articles/PMC2561161/
To LZ
plus this one:
//idconverter.bioinfo.cnio.es/
your
you
【在 j*p 的大作中提到】
: Try DAVID (there is KEGG pathway) or ingenuity pathway analysis and get your
: genelist ranked in someway. Instead of trying them one by one blindly, you
: need to kind of having an idea to try which ones first.
|
l**********1
发帖数: 5204 | 10 Oui.
Especially transporter protein/s whom might be/are relative to that/those target gene/s..
.
BTW, if you got break, BAO ZI One please transfer to my mitbbs financial account
W-E-I-B-I ten .
>回复]
0
[ 5 ]
发信人: aaaty (阿fan提), 信区: Biology
标 题: Re: 基因data mining很茫然啊
发信站: BBS 未名空间站 (Mon Mar 26 14:48:08 2012, 美东)
数据是已经被biostatistician/informatician分析过了
但是接下来就是要make sense那些基因真的有意义，这个貌似别人也没法帮忙
因为课题还是很新的领域，
所以之前lotkaeuler11的意思大概是放到network里面看看，如果我读懂了的话。 |
|
|
a***y
发帖数: 19743 | 11 I see. Thanks. I think the bioinformatician already tried to look at it from
pathway perspective and only found one pathway that seem to correlate, and
we are little puzzled by why that is the only one.
I can try the tools you mentioned. Ingenuity is kind of expensive, at lab
lunch they were talking about buying one license but I don't know what would
happen.
your
you
【在 j*p 的大作中提到】
: Try DAVID (there is KEGG pathway) or ingenuity pathway analysis and get your
: genelist ranked in someway. Instead of trying them one by one blindly, you
: need to kind of having an idea to try which ones first.
|
a***y
发帖数: 19743 | 12 what is your financial account?
lotkaeuler11?
target gene/s..
account
【在 l**********1 的大作中提到】
: Oui.
: Especially transporter protein/s whom might be/are relative to that/those target gene/s..
: .
: BTW, if you got break, BAO ZI One please transfer to my mitbbs financial account
: W-E-I-B-I ten .
: >回复]
: 0
: [ 5 ]
: 发信人: aaaty (阿fan提), 信区: Biology
: 标 题: Re: 基因data mining很茫然啊
|
a***y
发帖数: 19743 | 13 Thanks. this ID converter is super helpful
I was actually searching for a tool to convert affymetrix ID to other IDs.
【在 l**********1 的大作中提到】
: Bingo
: //www.ncbi.nlm.nih.gov/pmc/articles/PMC2561161/
: To LZ
: plus this one:
: //idconverter.bioinfo.cnio.es/
:
: your
: you
|
l**********1
发帖数: 5204 | 14 yes
【在 a***y 的大作中提到】
: what is your financial account?
: lotkaeuler11?
:
: target gene/s..
: account
|
l**********1
发帖数: 5204 | 15 De rien.
【在 a***y 的大作中提到】
: Thanks. this ID converter is super helpful
: I was actually searching for a tool to convert affymetrix ID to other IDs.
|
l**********1
发帖数: 5204 | 16 LZ你上哪个HUGO网站啦?
please go to:
//www.genenames.org/
or
//www.avatar.se/xref/wr/index
or
//www.ebi.ac.uk/uniprot/
then you never say that "HUGO上有什么resources，没看到啊" again
【在 a***y 的大作中提到】
: HUGO上有什么resources，没看到啊
:
: life_applications/data_minin
|
h*********c
发帖数: 78 | 17 ingenuity only makes you feel even more confused, trust me....david is a
good resource, there is another tool called toppsuite is another option |
