Hi, Vincent That's a good question. Currently, DO.obo file contains some synonyms for each DO term/ID. Our collaborators are working on curation right now. I'll talk to them about this. So far, what I can think is to retrieve the synonyms from DO.obo and use some text mining tools to find the DO ids. More info can be found at http://do-wiki.nubic.northwestern.edu/index.php/Main_Page And there will be a DO workshop between 2/8 and 2/9 at Baltimore. Best Gilbert On 1/28/11 2:25 PM, Vincent Carey wrote: > This has been an interesting discussion. A marginally connected > question: Are there tools to normalize found lists of symptoms that > use informal terminology so that they can be matched to formally > catalogued terms in DO? > > On Fri, Jan 28, 2011 at 9:57 AM, Ted Morrow<ted.morrow at="" ebc.uu.se=""> wrote: >> Hi Gilbert, >> >> Great thanks for the clarification....OK building myGA works fine and I have >> setAnnLib to org.Hs.eg.db with: >> myGA2<- setAnnLib(myGA, 'org.Hs.eg.db') >> getAnnLib(myGA2) >> [1] "org.Hs.eg.db" >> >> .....but at the geneAnswerReadable step: >> myGAreadable<- geneAnswersReadable(myGA2, catTerm=FALSE) >> >> I get the following error: >> [1] "Mapping geneInput ..." >> [1] "Warning: some genes do not have valid symbols!" >> [1] "Mapping genesInCategory ..." >> >> traceback() >> 2: stop(paste("The input geneAnswers categoryType is not DOLite but ", >> x at categoryType, ". stop function!")) >> 1: topDOLiteGenes(myGA, orderby = "pvalue", topGenes = "ALL", genesOrderBy = >> "pValue", >> file = TRUE) >> >> Cheers >> Ted >> >> sessionInfo() >> R version 2.12.1 (2010-12-16) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] org.Hs.eg.db_2.4.6 GeneAnswers_1.6.0 RColorBrewer_1.0-2 >> Heatplus_1.20.0 rgl_0.92.798 MASS_7.3-9 RSQLite_0.9-4 >> DBI_0.2-5 XML_3.2-0.2 annotate_1.28.0 >> AnnotationDbi_1.12.0 >> [12] Biobase_2.10.0 RCurl_1.5-0.1 bitops_1.0-4.1 >> igraph_0.5.5-1 >> >> loaded via a namespace (and not attached): >> [1] graph_1.28.0 grid_2.12.1 RBGL_1.26.0 Rgraphviz_1.27.0 >> tools_2.12.1 xtable_1.5-6 >>> >> >> >> >> On 1/28/2011 3:40 PM, Gilbert Feng wrote: >>> >>> Hi, Ted >>> >>> Yes, your codes about mygenepool and mygenes are correct. I didn't clearly >>> state them in my previous email. Sorry about that. myDOLite should be built >>> by DOLite and mygenepool, not mygenes. So currently, myDOLite is a >>> customized annotation library and when you build a geneAnswers instance, >>> leave categoryType to NULL(default value), and in your case, I think the >>> total gene number should be 1310, not 1202, since the former is the gene >>> number of mygenepool. >>> >>> after buiding myGA, run setAnnLib to set it to org.Hs.eg.db I guess the >>> error is that you don't set it. >>> >>> For the further mapping function, like geneAnswerReadable or other >>> visualization, always set catTerm=FALSE. >>> >>> Let me know if it doesn't work. >>> >>> Best >>> >>> Gilbert >>> >>> >>>> I have two gene pools - one is a universe of genes (called say >>>> "mygenepool") which is only a subset on all human genes, the other is a >>>> subset of mygenepool (called say "mygenes"). I am interested in knowing >>>> which DO terms show over-representation in mygenes given the DO terms >>>> present in mygenepool. So, in your example I am a bit confused as to >>>> which pool "mygenes" refers to. Is it "mygenepool" or "mygenes"? >>>> >>>> So I have...... >>>> str(mygenepool) # I used as.matrix then as.vector to change the >>>> dataframe into a vector...is that OK? >>>> int [1:1310] 8813 3075 2729 8379 204 170302 10165 6521 799 3052 ... >>>> >>>> and >>>> str(mygenes) >>>> int [1:1202] 6833 10083 60528 8842 5048 4843 6329 5080 6401 6853 ... >>>> >>>> >>>> and mygenes is a subset of mygenepool: >>>> overlap<- intersect(mygenepool, mygenes) >>>> str(overlap) >>>> int [1:1202] 6833 10083 60528 8842 5048 4843 6329 5080 6401 6853 ... >>>> >>>> >>>> Running the first bit of your example code seems to work fine: >>>> myDOLite<- lapply(DOLite, intersect, mygenepool) >>>> names(myDOLite)<- DOLiteTerm[names(myDOLite)] >>>> >>>> and so does creating a GeneAnswers instance (myGA) whether I specify the >>>> totalGeneNumber or not: >>>> myGA<- geneAnswersBuilder(mygenes, myDOLite, categoryType='DOLITE', >>>> testType='hyperG', >>>> #known=FALSE, totalGeneNumber=1202, >>>> pvalueT=0.1, geneExpressionProfile=NULL, verbose=TRUE) >>>> >>>> But then I get the following error: >>>> myGAreadable<- geneAnswersReadable(myGA, verbose=TRUE) >>>> [1] "Mapping geneInput ..." >>>> Error in switch(sub("org.*[:.:]", "", libname), eg = "EG", tair = "TAIR", >>>> : >>>> EXPR must be a length 1 vector >>>> >>>> traceback() >>>> 2: getSymbols(as.vector(x at geneInput[, 1]), x at annLib, strict = strict, >>>> missing = missing) >>>> 1: geneAnswersReadable(myGA, verbose = TRUE) >>>> >>>> If I instead create the GeneAnswers instance with 'org.Hs.eg.db' and not >>>> myDOLite the step..... >>>> myGAreadable<- geneAnswersReadable(myGA, verbose=TRUE) >>>> >>>> .....works fine as do later steps (for example geneAnsersChartPlots and >>>> topDOLiteGenes) >>>> >>>> But then presumably I am not working with the restricted pool of genes >>>> that I want to (i.e. mygenepool) >>>> >>>> Any ideas? >>>> Cheers >>>> Ted >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 1/27/2011 5:19 PM, Gilbert Feng wrote: >>>>> >>>>> Hi, Ted >>>>> >>>>> If I correctly understand your question, you have your own gene pool, >>>>> don't you? In that case, GeneAnswers still can handle that. What you >>>>> need is to build a customized DOLite list to run analysis. For example, >>>>> >>>>> if your genes are mygenes(an unique Entrez GENE ID vector) >>>>> >>>>> myDOLite<- lapply(DOLite, intersect, mygenes) >>>>> names(myDOLite)<- DOLiteTerm[names(myDOLite)] >>>>> #Please note that the parameter 'known' is TRUE in geneAnswersBuilder, >>>>> which means the test will only use shared genes in mygenes and DOLite >>>>> genes as the gene pool to run hypergeometric test. You can change the >>>>> number of gene pool by set parameter 'totalGeneNumber' and set 'known' >>>>> to FALSE at the same time . >>>>> myGA<- geneAnswersBuilder(mygenes, myDOLite, testType='hyperG', ...) >>>>> >>>>> since DO is designed for human, you can use setAnnLib to set the >>>>> species as 'org.Hs.eg.db' for further visualization or analysis. >>>>> >>>>> Let me know if you have any question. >>>>> >>>>> Gilbert >>>>> >>>>> BTW, the current one has a new function to automatically generate a >>>>> report for a or several groups of genes. Please check "groupReport" >>>>> page, but before you run it, make sure you have java support and flash >>>>> installation. >>>>> >>>>> >>>>> On 1/27/11 9:45 AM, Ted Morrow wrote: >>>>>> >>>>>> Thanks for your replies Gilbert and Peter.....I forgot to say in my >>>>>> original question that I did look into using both the GeneAnswers >>>>>> package and the FunDO web-based system but the issue I have not been >>>>>> able to solve with them is that I cannot specify "my gene Universe" >>>>>> within which my selected genes are tested for enrichment. I want to see >>>>>> which diseases are enriched out of the possible diseases in "my gene >>>>>> universe" which is a subset of all possible human genes. >>>>>> >>>>>> Is that possible in GeneAnswers (or even FunDO)? >>>>>> >>>>>> Cheers >>>>>> Ted >>>>>> >>>>>> On 1/27/2011 4:39 PM, Peter Robinson wrote: >>>>>>> >>>>>>> On 01/27/2011 04:17 PM, Gilbert Feng wrote: >>>>>>>> >>>>>>>> Hi, Ted >>>>>>>> >>>>>>>> DO.db is a standard sqlite file and you can use standard RSQLite >>>>>>>> procedure to retrieve the information. Actually we do have a lite >>>>>>>> version of Disease Ontology, DOLite that removes some redundant >>>>>>>> nodes, >>>>>>>> integrated in GeneAnswers package, which also uses hypergeometric >>>>>>>> test >>>>>>>> to run enrichment analysis as well as automatically generated >>>>>>>> interactive(cytoscape web support) html summary for one or more >>>>>>>> groups >>>>>>>> of genes. >>>>>>>> >>>>>>>> Best >>>>>>>> >>>>>>>> Gilbert >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> You might also want to take a look at this website: >>>>>>> http://django.nubic.northwestern.edu/fundo/faq >>>>>>> which implements enrichment analysis using genes annotated to DO >>>>>>> terms. >>>>>>> -peter >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> On 1/27/11 5:00 AM, Ted Morrow wrote: >>>>>>>>> >>>>>>>>> Dear all, >>>>>>>>> >>>>>>>>> I would like to conduct a hypergeometric test on a list of genes but >>>>>>>>> using Disease Ontology instead of GO or KEGG terms. The package >>>>>>>>> "DO.db" >>>>>>>>> contains this information but I have been unable to find a way of >>>>>>>>> using >>>>>>>>> this database in conjunction with the "GOstats" package that I have >>>>>>>>> been >>>>>>>>> using. >>>>>>>>> >>>>>>>>> Has anyone attempted to run a hypergeometric test for Disease >>>>>>>>> Ontology >>>>>>>>> terms? Is there another package I could use? Or is there a way of >>>>>>>>> modifying the argument (if that's the right word) GOHyperGParams in >>>>>>>>> GOstats so that it can make use of the information in DO.db? >>>>>>>>> >>>>>>>>> Both the GO and KEGG analyses work fine: >>>>>>>>> ### GO chunk >>>>>>>>> params<- new("GOHyperGParams", >>>>>>>>> geneIds = selectedEntrezIds, universeGeneIds = entrezUniverse, >>>>>>>>> annotation = "hgu95av2.db", ontology="BP", >>>>>>>>> pvalueCutoff=0.01, conditional=FALSE, >>>>>>>>> testDirection="over") >>>>>>>>> hgOver<- hyperGTest(params) >>>>>>>>> >>>>>>>>> hgOver >>>>>>>>> Gene to GO BP test for over-representation >>>>>>>>> 2136 GO BP ids tested (15 have p< 0.01) >>>>>>>>> Selected gene set size: 112 >>>>>>>>> Gene universe size: 951 >>>>>>>>> Annotation package: hgu95av2 >>>>>>>>> >>>>>>>>> ### KEGG chunk >>>>>>>>> paramsKEGG<- new("KEGGHyperGParams", >>>>>>>>> geneIds = selectedEntrezIds, universeGeneIds = entrezUniverse, >>>>>>>>> annotation = "hgu95av2.db", >>>>>>>>> pvalueCutoff=0.01, >>>>>>>>> testDirection="over") >>>>>>>>> >>>>>>>>> hgOverKEGG<- hyperGTest(paramsKEGG) >>>>>>>>> hgOverKEGG >>>>>>>>> summary(hgOverKEGG) >>>>>>>>> >>>>>>>>> My data looks like this: >>>>>>>>> str(selectedEntrezIds) >>>>>>>>> chr [1:157] "60528" "6853" "10157" "5081" "389434" "6591" "7414" >>>>>>>>> "7546" >>>>>>>>> "3074" "6916" "6559" "23503" "8626" "6557" "38" "60" "9733" "113235" >>>>>>>>> "28962" "10269" "4069" "30835" "7018" ... >>>>>>>>> >>>>>>>>>> str(entrezUniverse) >>>>>>>>> chr [1:1310] "8813" "3075" "2729" "8379" "204" "170302" "10165" >>>>>>>>> "6521" >>>>>>>>> "799" "3052" "1387" "5244" "3674" "6833" "10083" "60528" "8842" >>>>>>>>> "5048" >>>>>>>>> "4843" "6329" "5080" "6401" "6853" ... >>>>>>>>> >>>>>>>>> My naive attempts to use DO have included: >>>>>>>>> paramsDO<- new("DOHyperGParams", >>>>>>>>> geneIds = selectedEntrezIds, universeGeneIds = entrezUniverse, >>>>>>>>> annotation = "DO.db", >>>>>>>>> pvalueCutoff=0.01, >>>>>>>>> testDirection="over") >>>>>>>>> >>>>>>>>> Which of course doesn't work and gives the following error: >>>>>>>>> Error in getClass(Class, where = topenv(parent.frame())) : >>>>>>>>> "DOHyperGParams" is not a defined class >>>>>>>>> >>>>>>>>>> traceback() >>>>>>>>> 3: stop(gettextf("\"%s\" is not a defined class", Class), domain = >>>>>>>>> NA) >>>>>>>>> 2: getClass(Class, where = topenv(parent.frame())) >>>>>>>>> 1: new("DOHyperGParams", geneIds = selectedEntrezIds, >>>>>>>>> universeGeneIds = >>>>>>>>> entrezUniverse, >>>>>>>>> annotation = "DO.db", pvalueCutoff = 0.01, testDirection = "over") >>>>>>>>> >>>>>>>>> >>>>>>>>> Replacing "GOHyperGParams" with "DOHyperGParams" also gives the >>>>>>>>> following error:.. >>>>>>>>> >>>>>>>>> hgOverDO<- hyperGTest(paramsDO) >>>>>>>>> Error in match.arg(ontology, c("BP", "CC", "MF")) : >>>>>>>>> 'arg' should be one of ?BP?, ?CC?, ?MF? >>>>>>>>> >>>>>>>>> traceback() >>>>>>>>> 10: stop(gettextf("'arg' should be one of %s", >>>>>>>>> paste(dQuote(choices), >>>>>>>>> collapse = ", ")), domain = NA) >>>>>>>>> 9: match.arg(ontology, c("BP", "CC", "MF")) >>>>>>>>> 8: getUniverseViaGo(p) >>>>>>>>> 7: universeBuilder(p) >>>>>>>>> 6: universeBuilder(p) >>>>>>>>> 5: .hyperGTestInternal(p) >>>>>>>>> 4: is(object, Cl) >>>>>>>>> 3: is(object, Cl) >>>>>>>>> 2: .valueClassTest(standardGeneric("hyperGTest"), >>>>>>>>> "HyperGResultBase", >>>>>>>>> "hyperGTest") >>>>>>>>> 1: hyperGTest(paramsDO) >>>>>>>>> >>>>>>>>> >>>>>>>>> Any help would be greatly appreciated. >>>>>>>>> /Ted >>>>>>>>> >>>>>>>>>> sessionInfo() >>>>>>>>> R version 2.12.1 (2010-12-16) >>>>>>>>> Platform: i386-pc-mingw32/i386 (32-bit) >>>>>>>>> >>>>>>>>> locale: >>>>>>>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>>>>>>>> States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C >>>>>>>>> LC_TIME=English_United States.1252 >>>>>>>>> >>>>>>>>> attached base packages: >>>>>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>>>>> >>>>>>>>> other attached packages: >>>>>>>>> [1] KEGG.db_2.4.5 DO.db_2.1.0 GO.db_2.4.5 hgu95av2.db_2.4.5 >>>>>>>>> org.Hs.eg.db_2.4.6 GOstats_2.16.0 RSQLite_0.9-4 DBI_0.2-5 >>>>>>>>> graph_1.28.0 >>>>>>>>> Category_2.16.0 AnnotationDbi_1.12.0 >>>>>>>>> [12] Biobase_2.10.0 >>>>>>>>> >>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>> [1] annotate_1.28.0 genefilter_1.32.0 GSEABase_1.12.2 RBGL_1.26.0 >>>>>>>>> splines_2.12.1 survival_2.36-2 tools_2.12.1 XML_3.2-0.2 xtable_1.5-6 >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioconductor mailing list >>>>>>>> Bioconductor at r-project.org >>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>> Search the archives: >>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>> . >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >> -- >> ___________________________________________________________________ _______________ >> >> Edward H. Morrow >> Department of Ecology and Evolution >> Animal Ecology (zooekologi) >> Evolutionary Biology Centre >> Uppsala University >> Norbyv?gen 18-D >> SE-752 36 Uppsala >> SWEDEN >> >> Email: ted.morrow at ebc.uu.se >> Tel: +46 18 471 2676 >> Fax +46 18 471 6484 >> Webpage: >> http://www.iee.uu.se/zooekol/default.php?type=personalpage&id=119&l ang=en >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- ----------------------------------------------- Gang (Gilbert) Feng, PhD Biomedical Informatics Center Robert H. Lurie Comprehensive Cancer Center Northwestern University 750 N. Lake Shore Drive, 11th Floor(11-175e) Chicago, IL 60611 Phone:312-503-2358 Email g-feng (at) northwestern.edu