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1、GO enrichment and Pathway analysis of genes/proteinsHUANGWhy? Gene/proteins from analysis with microarray or transcriptome sequencing or proteomics To find the critical genes/pathways and to explain the results/design further experimentsGene Ontology(GO)Gene Ontology: 国际标准化的基因功能分类体系GO有三个本体 1基因发挥的分子功
2、能（molecular function） 2细胞位置/组分（cellular component） 3参与的生物过程（biological process）http:/www.geneontology.org/How to do Enrichment?The GO has been annotated by the companies, but not all the genes are annotated(50% or more less).- BLAST2GO (http:/ g:Profiler (http:/biit.cs.ut.ee/gprofiler/welcome.cgi)-
3、argot (http:/www.medcomp.medicina.unipd.it/Argot2/index.php)- DAVID (http:/david.abcc.ncifcrf.gov/home.jsp)(sequences)(sequences)(sequences)(Gene ID/ Probe ID)(Gene ID/ Probe ID)How to do Enrichment?(Gene ID)- AgriGO http:/ 1: Get the Fasta format sequences (nt or pr)Way 1: Perl language （优先）Way 2:
4、from NCBI/GenBank必须提前知道基因或蛋白的注册号；如果是探针号可以通过一些序列号转 换程序（如DAVID，Affrimetrix)转换为NCBI识别的号码。BLAST2GOStep 1: Get the Fasta format sequences (nt or pr)BLAST2GOBLAST2GODAVIDDAVIDDAVIDKEGG pathway分析DAVIDKEGG pathway分析AGRIGOhttp:/ for pathway analysishttp:/ FASTA sequences and gene IDsKOBASKOBASGene ID 转换KOBAS
5、KOBASKOBASKOBASKOBASMapmanhttp:/mapman.mpimp-golm.mpg.de/需要JAVA平台，下载到本地后运行。主要是用芯片的探针编号。MapmanLoad data (*.xls)MapmanMapmanMapmanMapmanMapmanJAMapmanSecondary metabolismSummary GO enrichment and KEGG pathway analysis are popular in the analysis of microarray or transcriptome data.It is suggested to u
6、se AgriGO (for GO annotation, enrichment analysis) and KOBAS (for KEGG pathway analysis), and MapMan program (to map the differentially expressed genes in metabolism pathways).BLAST2GO is best for GO annotation analysis but too slow.DAVID is also powerful but the data updating is slow.WorkIn Class w
7、ork:(1) Copy the sequence ID (left, rice Affrimetrix probe ID);Use DAVID to convert the ID to Entrez gene ID;Use KOBAS to do pathway analysis. (2) Use AgriGo website to do GO enrichment analysis.Os.20851.1.A1_at Os.4184.1.S1_at Os.20851.1.A1_x_at Os.54747.1.S2_at Os.48948.1.S1_at Os.15737.1.S1_x_at
8、Os.48948.1.S1_x_at Os.10038.1.S1_s_at Os.10266.1.S1_at Os.53467.1.S1_at Os.4620.1.S1_at Os.38444.2.S1_at Os.6645.1.S1_at Os.9762.2.S1_at Os.20614.3.S1_x_at Os.6792.1.S1_at Os.46733.1.S1_at Os.54747.1.S1_at OsAffx.31235.1.S1_at OsAffx.28517.1.S1_at Os.9762.1.S1_at Os.51228.2.A1_at OsAffx.23902.2.S1_a
9、t Os.51339.1.S1_at Os.6645.1.S1_s_at OsAffx.5196.1.S1_at Os.50825.1.S1_s_at Os.51787.1.S1_at OsAffx.26155.1.S1_x_at Os.56924.1.S1_at Os.11920.1.S1_s_at OsAffx.24056.2.S1_at Os.26849.1.S1_at OsAffx.15407.1.S1_at Os.29043.1.S1_at Os.6863.1.S1_s_at Os.45510.1.S1_at Os.27804.1.S1_at OsAffx.17318.1.S1_at
10、 Os.20313.1.S1_s_at Os.57569.2.A1_s_at Os.51561.1.S1_at Os.6863.1.S1_at Os.19861.1.S1_at Os.45516.1.S1_at Os.27702.1.S1_x_at Os.15355.1.S1_x_at Os.6148.1.S1_at Os.34283.3.S1_at Os.46574.1.S1_at Os.56048.1.S1_s_at Os.27474.1.S1_at Os.32889.1.S1_at Os.9962.1.S1_s_at Os.15841.1.S1_a_at OsAffx.14657.1.S
11、1_at Os.46431.1.S1_at Os.46716.2.S1_at Os.40030.1.S1_s_at Os.5601.1.S1_at Os.57103.1.S1_at Os.35642.2.S1_x_at OsAffx.382.2.A1_at Os.6976.2.A1_at Os.52619.1.S1_at Os.20313.1.S1_x_at OsAffx.19103.1.S1_at Os.37969.2.S1_at Os.23518.1.A1_at Os.45916.1.S1_s_at Os.27292.1.A1_at Os.26728.3.S1_at Os.26820.1.
12、A1_s_at OsAffx.19309.1.S1_at OsAffx.13543.1.S1_s_at Os.5295.1.S1_at Os.2373.1.S1_at OsAffx.32292.1.A1_at OsAffx.31590.1.S1_at Os.23327.2.S1_a_at OsAffx.26321.1.S1_at Os.26852.1.A1_at OsAffx.15538.1.S1_at OsAffx.13954.1.S1_at OsAffx.26416.1.S1_at Os.33602.1.S2_at Os.10185.1.S1_at Os.9238.1.A1_a_at Os
13、.48074.1.A1_at Os.17900.1.S1_s_at Os.50501.1.S1_at Os.54226.1.S1_s_at Os.45041.1.S1_x_at OsAffx.19108.1.S1_x_at OsAffx.7460.1.S1_at Os.27098.2.A1_s_at OsAffx.30966.4.S1_x_at OsAffx.4094.1.S1_at OsAffx.11002.1.S1_at Os.27185.1.S1_x_at Os.19350.1.S1_at Os.41723.1.S1_at Os.17158.1.S1_at Os.48268.1.S1_a
14、t Os.49536.1.S1_at Os.17316.1.S1_at OsAffx.18105.1.S1_at OsAffx.31756.1.S1_at Os.53606.1.S1_at Os.49826.1.S1_at Os.37565.1.S1_at OsAffx.3726.1.S1_at Os.4844.1.S1_at Os.53055.1.S1_at Os.18913.2.S1_at Os.51078.1.S1_at Os.26941.1.A1_at OsAffx.8759.1.S1_at Os.27215.1.A2_at OsAffx.27093.1.S1_at Os.56290.
15、1.S1_at Os.52282.1.S1_at Os.14210.1.S1_at Os.50222.1.S1_at Os.51405.1.S1_at OsAffx.29832.2.S1_s_at OsAffx.26349.1.S1_at OsAffx.30677.5.S1_x_at Os.18503.1.S1_s_at Os.40417.1.A1_at OsAffx.12740.1.S1_s_at Os.33874.2.A1_x_at Os.49453.1.S1_at Os.8458.1.S1_s_at Os.12988.1.S1_at Os.9778.1.S1_at Os.33762.1.S1_at Os.5816.1.S1_at OsAffx.16737.1.S1_at Os.6786.1.S1_a_at Os.26957.1.A1_a_at Os.9778.1.S2_at OsAffx.7183.1.S1_s_at Os.38113.1.S2_
