Answers.Body: <p>I guess plasmodium doesn't have that many online tools dedicated to it so you can use the annotation packages from bioconductor and try it. I used clusterProfiler for analysis and org.Pf.plasmo.db for annotation below.</p>
  
  <p>From <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5257-x#MOESM4" rel="nofollow noreferrer">this paper</a>, grabbed table 1, a table of supposed genes involved in something: </p>
  
  <pre><code>genes = c("PF3D7_1302100", "PF3D7_0501300", "PF3D7_0302500*", "PF3D7_1030200", 
  "PF3D7_0302200*", "PF3D7_1327300", "PF3D7_0410000", "PF3D7_0104300", 
  "PF3D7_0420300", "PF3D7_0810000*", "PF3D7_0522300", "PF3D7_0935700*", 
  "PF3D7_0424700*", "PF3D7_1477700*", "PF3D7_0202000*", "PF3D7_1371600", 
  "PF3D7_1036300", "PF3D7_0422900", "PF3D7_0501400", "PF3D7_0221700", 
  "PF3D7_0301000", "PF3D7_1454100", "PF3D7_0831800", "PF3D7_0424900", 
  "PF3D7_1447500", "PF3D7_1477400", "PF3D7_0424800", "PF3D7_0823700", 
  "PF3D7_1477300", "PF3D7_0814100", "PF3D7_1372100", "PF3D7_0201500", 
  "PF3D7_0825300", "PF3D7_0201700", "PF3D7_1470000", "PF3D7_1401000", 
  "PF3D7_0724900", "PF3D7_0601700", "PF3D7_1410000", "PF3D7_0109300", 
  "PF3D7_1347300", "PF3D7_0201800", "PF3D7_1242100", "PF3D7_0403300", 
  "PF3D7_0114500", "PF3D7_1301200", "PF3D7_0931200", "PF3D7_0832200.1", 
  "PF3D7_0305900", "PF3D7_0608310", "PF3D7_0221800", "PF3D7_0511100", 
  "PF3D7_1001300", "PF3D7_1225900", "PF3D7_1444600", "PF3D7_1349900", 
  "PF3D7_1008300", "PF3D7_0919600", "PF3D7_1210300", "PF3D7_0929700", 
  "PF3D7_0701600", "PF3D7_0201600", "PF3D7_0801600", "PF3D7_1463600", 
  "PF3D7_0201900", "PF3D7_0905000", "PF3D7_1310000", "PF3D7_0315200", 
  "PF3D7_1139200", "PF3D7_1023500", "PF3D7_1111300", "PF3D7_0930700", 
  "PF3D7_1350800", "PF3D7_0412300", "PF3D7_0831900", "PF3D7_0406600", 
  "PF3D7_1448100", "PF3D7_0114300", "PF3D7_0526100", "PF3D7_1243200", 
  "PF3D7_0921100", "PF3D7_0301900", "PF3D7_0622700", "PF3D7_0811800", 
  "PF3D7_0114200", "PF3D7_0221500", "PF3D7_1129850", "PF3D7_1142200", 
  "PF3D7_0114100", "PF3D7_0512900", "PF3D7_1346200", "PF3D7_1369400", 
  "PF3D7_0314300", "PF3D7_0324100", "PF3D7_0107700", "PF3D7_1122000", 
  "PF3D7_0618800", "PF3D7_0601200", "PF3D7_1360300", "PF3D7_1318500", 
  "PF3D7_1111700", "PF3D7_0901900", "PF3D7_1313900", "PF3D7_1101700", 
  "PF3D7_1313200", "PF3D7_1039700", "PF3D7_0222100", "PF3D7_1371500", 
  "PF3D7_1344700", "PF3D7_1408300", "PF3D7_0929800", "PF3D7_0115000", 
  "PF3D7_1462900", "PF3D7_1352600", "PF3D7_0626200", "PF3D7_0831750", 
  "PF3D7_0602300", "PF3D7_0521100", "PF3D7_1452100", "PF3D7_0718900", 
  "PF3D7_0101300", "PF3D7_0815700", "PF3D7_0113600", "PF3D7_0937200", 
  "PF3D7_1108800", "PF3D7_0221100", "PF3D7_0921500", "PF3D7_1038300", 
  "PF3D7_0201400", "PF3D7_0822200", "PF3D7_0937000", "PF3D7_0301100"
  )
  </code></pre>
  
  <p>We can for example using clusterProfiler:</p>
  
  <pre><code>library(org.Pf.plasmo.db)
  library(clusterProfiler)
  </code></pre>
  
  <p>Besides the list of interest, you need to get a "universe" of all genes tested, in your situation it will be genes that you tested for differential gene expression, below I used all the genes annotated:</p>
  
  <pre><code>geneList = keys(org.Pf.plasmo.db)
  
  enr &lt;- enrichGO(genes,universe=geneList, OrgDb='org.Pf.plasmo.db', 
  keyType ="SYMBOL",ont="BP")
  </code></pre>
  
  <p>Above is a GO term enrichment, biological processes, you can look at the result like this:</p>
  
  <pre><code>head(enr@result,readtable=TRUE)
                         ID
      GO:0042000 GO:0042000
      GO:0044417 GO:0044417
      GO:0044766 GO:0044766
      GO:0051808 GO:0051808
      GO:0051836 GO:0051836
      GO:1902579 GO:1902579
                                                                                                 Description
      GO:0042000                                             translocation of peptides or proteins into host
      GO:0044417                                                        translocation of molecules into host
      GO:0044766                                                                    multi-organism transport
      GO:0051808 translocation of peptides or proteins into other organism involved in symbiotic interaction
      GO:0051836            translocation of molecules into other organism involved in symbiotic interaction
      GO:1902579                                                                 multi-organism localization
  </code></pre>
  
  <p>And you can plot it:</p>
  
  <pre><code>dotplot(enr)
  </code></pre>
  
  <p><a href="https://i.sstatic.net/jSfQr.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/jSfQr.png" alt="enter image description here"></a></p>
  
  <p>You can read more about the analysis you can do at the package <a href="https://yulab-smu.github.io/clusterProfiler-book/" rel="nofollow noreferrer">website</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-07T06:40:34.967Z
Answers.Text: genes = c("PfDd2_090042100*", "PfDd2_060005300*","PfDd2_020024700*","PfDd2_050038200*", "PfDd2_130078600*","PfDd2_050037500*",
            "PfDd2_060005700*","PfDd2_120045400*" )                                                                                             --> No gene can be mapped....
  --> Expected input gene ID: PF3D7_1405400,PF3D7_0623400,PF3D7_1025600,PF3D7_1439000,PF3D7_1423000,PF3D7_0716100
  --> return NULL...
Answers.UserDisplayName: Diango
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-07T06:43:41.873Z
Answers.Text: Apparently in this database there is no emotion that matches my gene_id (pdDd2_xxxxx) instead of PF3D7_xxxxxx. ps: I am working on the Dd2 strain of the parasite and not the 3D7 strain
Answers.UserDisplayName: Diango
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-07T08:29:12.290Z
Answers.Text: Anyway you can map it to the PF3D7? For pathway etc analysis, you are as good as your annotation. I am not so familiar with plasmodium, but surely somehow must have encountered this problem?
Answers.UserDisplayName: StupidWolf
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-07T09:35:21.540Z
Answers.Text: Okey thank you very much for your suggestions I will resume the annotation with 3D7
Answers.UserDisplayName: Diango
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-06T23:37:04.703Z
Answers.LastActivityDate: 2020-04-06T23:37:04.703Z
Answers.UserDisplayName: StupidWolf
Body: <p>I have genes differentially expressed between two groups (case and control). I would like to annotate them by classifying them according to their biological functions.</p>
  
  <p>I work on parasites of Plasmodium Falciparum type Dd2 which are divided into two groups (case and control). I carried out a Differential expression analysis with cuffdiff and CummeRbund then I annotated my genes on plasmodb.org.</p>
  
  <p>Example of id genes: pfDd2_14005040</p>
  
  <p>Now I would like to do a pathway analysis to see which biological pathways these genes are involved in.</p>
  
  <p>StupidWolf,
  I resumed my annotation with the 3D7 strain of plasmoduim Falciparum then I created my geneList as you indicated but when I make the dotplot nothing is displayed</p>
  
  <pre><code>setwd("C:/cygwin64/home/DIANGO/EXCELL")
  library(org.Pf.plasmo.db)
  library(clusterProfiler)
  
  gene &lt;- c ("PF3D7_0936800","PF3D7_1478900","PF3D7_1009700","PF3D7_0508500")
  geneList = keys(org.Pf.plasmo.db)
  enr &lt;- enrichGO(gene,universe=geneList,OrgDb='org.Pf.plasmo.db',keyType ="SYMBOL",ont="BP")
  head(enr@result,readtable=TRUE)
  dotplot(enr)
  
  </code></pre>
  
  <p>The output gives a white rectangle</p>
  
  <pre><code>                   ID                           Description GeneRatio  BgRatio     pvalue
  GO:0006323 GO:0006323                         DNA packaging       1/2  21/2615 0.01599974
  GO:0071103 GO:0071103               DNA conformation change       1/2  30/2615 0.02281728
  GO:0051276 GO:0051276               chromosome organization       1/2  58/2615 0.04387582
  GO:0006996 GO:0006996                organelle organization       1/2 144/2615 0.10712138
  GO:0016043 GO:0016043       cellular component organization       1/2 203/2615 0.14925925
  GO:0006464 GO:0006464 cellular protein modification process       1/2 265/2615 0.19244223
              p.adjust     qvalue        geneID Count
  GO:0006323 0.1026777 0.07205456 PF3D7_0508500     1
  GO:0071103 0.1026777 0.07205456 PF3D7_0508500     1
  GO:0051276 0.1316275 0.09237015 PF3D7_0508500     1
  GO:0006996 0.2203602 0.15463872 PF3D7_0508500     1
  GO:0016043 0.2203602 0.15463872 PF3D7_0508500     1
  GO:0006464 0.2203602 0.15463872 PF3D7_1009700     1
  &gt; dotplot(enr)
  
  </code></pre>
  
  <p><a href="https://i.sstatic.net/3PMyb.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/3PMyb.png" alt="enter image description here"></a></p>
  
  <p>Once again I need your help. </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-06T19:51:52.257Z
Comments.Text: I used webtools like:
  
  DAVID, Reactome, panther.
  
  
  But they all tell me that my id genes are not in the right format. I made my annotations on plasmodb.org
Comments.UserDisplayName: Diango
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-06T22:57:30.930Z
Comments.Text: i think david,etc might not have plasmodium annotations, so they cannot map your gene id to pathways... you use this.. http://bioconductor.org/packages/release/data/annotation/html/org.Pf.plasmo.db.html
Comments.UserDisplayName: StupidWolf
Tags: <rna-seq><differential-expression><functional-annotation>
Title: Differential Expression
ThreadText: # Differential Expression
  
  (Asked by: username_0 on 2020-04-06)
  
  I have genes differentially expressed between two groups (case and control). I would like to annotate them by classifying them according to their biological functions.
  
  I work on parasites of Plasmodium Falciparum type Dd2 which are divided into two groups (case and control). I carried out a Differential expression analysis with cuffdiff and CummeRbund then I annotated my genes on plasmodb.org.
  
  Example of id genes: pfDd2\_14005040
  
  Now I would like to do a pathway analysis to see which biological pathways these genes are involved in.
  
  username_1,
  I resumed my annotation with the 3D7 strain of plasmoduim Falciparum then I created my geneList as you indicated but when I make the dotplot nothing is displayed
  
  ```
  setwd("C:/cygwin64/home/username_0/EXCELL")
  library(org.Pf.plasmo.db)
  library(clusterProfiler)
  
  gene <- c ("PF3D7_0936800","PF3D7_1478900","PF3D7_1009700","PF3D7_0508500")
  geneList = keys(org.Pf.plasmo.db)
  enr <- enrichGO(gene,universe=geneList,OrgDb='org.Pf.plasmo.db',keyType ="SYMBOL",ont="BP")
  head(enr@result,readtable=TRUE)
  dotplot(enr)
  
  ```
  
  The output gives a white rectangle
  
  ```
                     ID                           Description GeneRatio  BgRatio     pvalue
  GO:0006323 GO:0006323                         DNA packaging       1/2  21/2615 0.01599974
  GO:0071103 GO:0071103               DNA conformation change       1/2  30/2615 0.02281728
  GO:0051276 GO:0051276               chromosome organization       1/2  58/2615 0.04387582
  GO:0006996 GO:0006996                organelle organization       1/2 144/2615 0.10712138
  GO:0016043 GO:0016043       cellular component organization       1/2 203/2615 0.14925925
  GO:0006464 GO:0006464 cellular protein modification process       1/2 265/2615 0.19244223
              p.adjust     qvalue        geneID Count
  GO:0006323 0.1026777 0.07205456 PF3D7_0508500     1
  GO:0071103 0.1026777 0.07205456 PF3D7_0508500     1
  GO:0051276 0.1316275 0.09237015 PF3D7_0508500     1
  GO:0006996 0.2203602 0.15463872 PF3D7_0508500     1
  GO:0016043 0.2203602 0.15463872 PF3D7_0508500     1
  GO:0006464 0.2203602 0.15463872 PF3D7_1009700     1
  > dotplot(enr)
  
  ```
  
  [![enter image description here](https://i.sstatic.net/3PMyb.png)](https://i.sstatic.net/3PMyb.png)
  
  Once again I need your help.
  
  **Tags:** rna-seq, differential-expression, functional-annotation
  
  > **Comments:**
  > **username_0**: I used webtools like:  DAVID, Reactome, panther.   But they all tell me that my id genes are not in the right format. I made my annotations on plasmodb.org  
  > **username_1**: i think david,etc might not have plasmodium annotations, so they cannot map your gene id to pathways... you use this.. http://bioconductor.org/packages/release/data/annotation/html/org.Pf.plasmo.db.html  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-04-06. Score: 1
  
  I guess plasmodium doesn't have that many online tools dedicated to it so you can use the annotation packages from bioconductor and try it. I used clusterProfiler for analysis and org.Pf.plasmo.db for annotation below.
  
  From [this paper](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5257-x#MOESM4), grabbed table 1, a table of supposed genes involved in something:
  
  ```
  genes = c("PF3D7_1302100", "PF3D7_0501300", "PF3D7_0302500*", "PF3D7_1030200", 
  "PF3D7_0302200*", "PF3D7_1327300", "PF3D7_0410000", "PF3D7_0104300", 
  "PF3D7_0420300", "PF3D7_0810000*", "PF3D7_0522300", "PF3D7_0935700*", 
  "PF3D7_0424700*", "PF3D7_1477700*", "PF3D7_0202000*", "PF3D7_1371600", 
  "PF3D7_1036300", "PF3D7_0422900", "PF3D7_0501400", "PF3D7_0221700", 
  "PF3D7_0301000", "PF3D7_1454100", "PF3D7_0831800", "PF3D7_0424900", 
  "PF3D7_1447500", "PF3D7_1477400", "PF3D7_0424800", "PF3D7_0823700", 
  "PF3D7_1477300", "PF3D7_0814100", "PF3D7_1372100", "PF3D7_0201500", 
  "PF3D7_0825300", "PF3D7_0201700", "PF3D7_1470000", "PF3D7_1401000", 
  "PF3D7_0724900", "PF3D7_0601700", "PF3D7_1410000", "PF3D7_0109300", 
  "PF3D7_1347300", "PF3D7_0201800", "PF3D7_1242100", "PF3D7_0403300", 
  "PF3D7_0114500", "PF3D7_1301200", "PF3D7_0931200", "PF3D7_0832200.1", 
  "PF3D7_0305900", "PF3D7_0608310", "PF3D7_0221800", "PF3D7_0511100", 
  "PF3D7_1001300", "PF3D7_1225900", "PF3D7_1444600", "PF3D7_1349900", 
  "PF3D7_1008300", "PF3D7_0919600", "PF3D7_1210300", "PF3D7_0929700", 
  "PF3D7_0701600", "PF3D7_0201600", "PF3D7_0801600", "PF3D7_1463600", 
  "PF3D7_0201900", "PF3D7_0905000", "PF3D7_1310000", "PF3D7_0315200", 
  "PF3D7_1139200", "PF3D7_1023500", "PF3D7_1111300", "PF3D7_0930700", 
  "PF3D7_1350800", "PF3D7_0412300", "PF3D7_0831900", "PF3D7_0406600", 
  "PF3D7_1448100", "PF3D7_0114300", "PF3D7_0526100", "PF3D7_1243200", 
  "PF3D7_0921100", "PF3D7_0301900", "PF3D7_0622700", "PF3D7_0811800", 
  "PF3D7_0114200", "PF3D7_0221500", "PF3D7_1129850", "PF3D7_1142200", 
  "PF3D7_0114100", "PF3D7_0512900", "PF3D7_1346200", "PF3D7_1369400", 
  "PF3D7_0314300", "PF3D7_0324100", "PF3D7_0107700", "PF3D7_1122000", 
  "PF3D7_0618800", "PF3D7_0601200", "PF3D7_1360300", "PF3D7_1318500", 
  "PF3D7_1111700", "PF3D7_0901900", "PF3D7_1313900", "PF3D7_1101700", 
  "PF3D7_1313200", "PF3D7_1039700", "PF3D7_0222100", "PF3D7_1371500", 
  "PF3D7_1344700", "PF3D7_1408300", "PF3D7_0929800", "PF3D7_0115000", 
  "PF3D7_1462900", "PF3D7_1352600", "PF3D7_0626200", "PF3D7_0831750", 
  "PF3D7_0602300", "PF3D7_0521100", "PF3D7_1452100", "PF3D7_0718900", 
  "PF3D7_0101300", "PF3D7_0815700", "PF3D7_0113600", "PF3D7_0937200", 
  "PF3D7_1108800", "PF3D7_0221100", "PF3D7_0921500", "PF3D7_1038300", 
  "PF3D7_0201400", "PF3D7_0822200", "PF3D7_0937000", "PF3D7_0301100"
  )
  
  ```
  
  We can for example using clusterProfiler:
  
  ```
  library(org.Pf.plasmo.db)
  library(clusterProfiler)
  
  ```
  
  Besides the list of interest, you need to get a "universe" of all genes tested, in your situation it will be genes that you tested for differential gene expression, below I used all the genes annotated:
  
  ```
  geneList = keys(org.Pf.plasmo.db)
  
  enr <- enrichGO(genes,universe=geneList, OrgDb='org.Pf.plasmo.db', 
  keyType ="SYMBOL",ont="BP")
  
  ```
  
  Above is a GO term enrichment, biological processes, you can look at the result like this:
  
  ```
  head(enr@result,readtable=TRUE)
                         ID
      GO:0042000 GO:0042000
      GO:0044417 GO:0044417
      GO:0044766 GO:0044766
      GO:0051808 GO:0051808
      GO:0051836 GO:0051836
      GO:1902579 GO:1902579
                                                                                                 Description
      GO:0042000                                             translocation of peptides or proteins into host
      GO:0044417                                                        translocation of molecules into host
      GO:0044766                                                                    multi-organism transport
      GO:0051808 translocation of peptides or proteins into other organism involved in symbiotic interaction
      GO:0051836            translocation of molecules into other organism involved in symbiotic interaction
      GO:1902579                                                                 multi-organism localization
  
  ```
  
  And you can plot it:
  
  ```
  dotplot(enr)
  
  ```
  
  [![enter image description here](https://i.sstatic.net/jSfQr.png)](https://i.sstatic.net/jSfQr.png)
  
  You can read more about the analysis you can do at the package [website](https://yulab-smu.github.io/clusterProfiler-book/)
  
  > **Comments:**
  > **username_0**: genes = c("PfDd2_090042100*", "PfDd2_060005300*","PfDd2_020024700*","PfDd2_050038200*", "PfDd2_130078600*","PfDd2_050037500*",           "PfDd2_060005700*","PfDd2_120045400*" )                                                                                             --> No gene can be mapped.... --> Expected input gene ID: PF3D7_1405400,PF3D7_0623400,PF3D7_1025600,PF3D7_1439000,PF3D7_1423000,PF3D7_0716100 --> return NULL...  
  > **username_0**: Apparently in this database there is no emotion that matches my gene_id (pdDd2_xxxxx) instead of PF3D7_xxxxxx. ps: I am working on the Dd2 strain of the parasite and not the 3D7 strain  
  > **username_1**: Anyway you can map it to the PF3D7? For pathway etc analysis, you are as good as your annotation. I am not so familiar with plasmodium, but surely somehow must have encountered this problem?  
  > **username_0**: Okey thank you very much for your suggestions I will resume the annotation with 3D7  
  
  ---
  
  