Article View: bionet.software
Article #2501Re: [Bio-software] Please recommend good ontology analysis tools
From: Robert Miles
Date: Sat, 31 Jul 2010 15:21
Date: Sat, 31 Jul 2010 15:21
37 lines
3475 bytes
3475 bytes
"RY Bao" <ry_bao@yahoo.com> wrote in message news:mailman.936.1280460013.25217.bio-soft@net.bio.net... > Hello Everybody, > > I have a list of about 6000 genes, with around 800 of them associated with > gene > family expansion. I want to detect GO over/under-representation in this > dataset. > I have tried GOstat (FDR Benjamini), GOToolBox (Hypergeometric, Benjamini > & > Hochberg), and Ontologizer (Parent-Child-Union, Benjamini-Hochberg). > However, > they gave me very different results. Could anybody give me some > suggestions > about which program to use, or which model gives better results? Are there > any > other recommended programs that I can use? Thank you so much! :-) > > Greetings, > Sunny Bao (Wayne State University, US) I've found two BOINC projects associated with genetic research, but not the corresponding ways to submit work for them to do. http://cbl-boinc-server2.cs.technion.ac.il/superlinkattechnion/ Located in Israel; mostly human genetic research. http://boinc.bio.wzw.tum.de/boincsimap/ Located in Germany; mostly comparisons of protein sequences from different species, but also some comparisons of genetic sequences from different species. I've seen little sign that either of them will make their software available for use elsewhere. Robert Miles
Technical Details
Message-ID:
<mailman.939.1280593156.25217.bio-soft@net.bio.net>Path:
arc1-ca.pugleaf.net!g2news1.google.com!news3.google.com!news2.google.com!Xl.tags.giganews.com!border1.nntp.dca.giganews.com!nntp.giganews.com!local2.nntp.dca.giganews.com!news.giganews.com.POSTED!not-for-mailReferences:
<mailman.936.1280460013.25217.bio-soft@net.bio.net>Show Full Headers
Complete Article Headers
X-Google-Thread: fa6b6,fd2dc8709623ff06 X-Google-NewGroupId: yes X-Google-Attributes: gid6710630482,domainid0,public,usenet X-Google-Language: ENGLISH,ASCII-7-bit Path: arc1-ca.pugleaf.net!g2news1.google.com!news3.google.com!news2.google.com!Xl.tags.giganews.com!border1.nntp.dca.giganews.com!nntp.giganews.com!local2.nntp.dca.giganews.com!news.giganews.com.POSTED!not-for-mail NNTP-Posting-Date: Sat, 31 Jul 2010 11:19:45 -0500 X-Envelope-From: news@highwinds-media.com To: bionet-software@moderators.isc.org From: "Robert Miles" <milesrf@usenet-news.net> References: <mailman.936.1280460013.25217.bio-soft@net.bio.net> In-Reply-To: <mailman.936.1280460013.25217.bio-soft@net.bio.net> X-Priority: 3 X-MSMail-Priority: Normal Importance: Normal X-Newsreader: Microsoft Windows Live Mail 14.0.8117.416 X-MimeOLE: Produced By Microsoft MimeOLE V14.0.8117.416 X-RFC2646: Format=Flowed; Original Date: Sat, 31 Jul 2010 10:21:13 -0500 X-Mailman-Approved-At: Sat, 31 Jul 2010 11:19:14 -0500 X-BeenThere: bio-soft@net.bio.net X-Mailman-Version: 2.1.4 Precedence: list Organization: BIOSCI/IUBio, Biology Dept., Indiana University subject: Re: [Bio-software] Please recommend good ontology analysis tools Newsgroups: bionet.software Message-ID: <mailman.939.1280593156.25217.bio-soft@net.bio.net> Approved: BIOSCI Approval Key <biosci-approval-key@net.bio.net> X-Auth: PGPMoose V1.1 PGP bionet.software iQCVAwUBTFRNBaCIqsWvyF5FAQFZyAP8D6n8bwi3B8cAOMDhMTPe+KV1nPopvmba 3fq6PJIptrMaSxVniwtBeyQoGNM9Zop5vPXviYnCbZHVWPOeIw6yg+GpT96S9jhD ozXt9rpETgZKpjDrRjbG9NiQlrlUe7/rzDQyPm28sQQUd219M2viUYelLp1/RB8O xWhIxO5KWAo= =GbBn Lines: 38 X-Usenet-Provider: http://www.giganews.com X-Trace: sv3-UlzKhxY4e4IHzMYZi4Yd7ErAg4ZCdbfHYSDtEeAWECLU69NfZImm/nKc3qymnA10e46RzP1CMNGtGMH!tmSTZUp/xpCaauxH9LDkue4gCfoV0AfBtudKocuFNu07pUbARqB1L+9MtgCK9Ee5Rumb4C94HwXK!5qxD X-Complaints-To: abuse@giganews.com X-DMCA-Notifications: http://www.giganews.com/info/dmca.html X-Abuse-and-DMCA-Info: Please be sure to forward a copy of ALL headers X-Abuse-and-DMCA-Info: Otherwise we will be unable to process your complaint properly X-Postfilter: 1.3.40