ReactomePA is designed for reactome pathway based analysis (Yu and He 2016 ) . Reactome is an open-source, open access, manually curated and peer-reviewed pathway database.
Supported organisms
Currently ReactomePA supports several model organisms, including ‘celegans’, ‘fly’, ‘human’, ‘mouse’, ‘rat’, ‘yeast’ and ‘zebrafish’. The input gene ID should be Entrez gene ID. We recommend using clusterProfiler::bitr()
Reactome pathway over-representation analysis
Enrichment analysis is a widely used approach to identify biological themes. ReactomePA implemented enrichPathway() hypergeometric model to assess whether the number of selected genes associated with a reactome pathway is larger than expected.
[1] "4312" "8318" "10874" "55143" "55388" "991"
ID
R-HSA-69278 R-HSA-69278
R-HSA-69620 R-HSA-69620
R-HSA-69618 R-HSA-69618
R-HSA-2500257 R-HSA-2500257
R-HSA-141424 R-HSA-141424
R-HSA-141444 R-HSA-141444
Description
R-HSA-69278 Cell Cycle, Mitotic
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-69618 Mitotic Spindle Checkpoint
R-HSA-2500257 Resolution of Sister Chromatid Cohesion
R-HSA-141424 Amplification of signal from the kinetochores
R-HSA-141444 Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
GeneRatio BgRatio RichFactor FoldEnrichment zScore
R-HSA-69278 49/314 479/10173 0.1022965 3.314210 9.259137
R-HSA-69620 33/314 244/10173 0.1352459 4.381709 9.541792
R-HSA-69618 19/314 94/10173 0.2021277 6.548550 9.644646
R-HSA-2500257 20/314 109/10173 0.1834862 5.944604 9.262132
R-HSA-141424 17/314 79/10173 0.2151899 6.971741 9.508990
R-HSA-141444 17/314 79/10173 0.2151899 6.971741 9.508990
pvalue p.adjust qvalue
R-HSA-69278 6.635185e-14 5.288243e-11 4.742411e-11
R-HSA-69620 5.785253e-13 2.305423e-10 2.067467e-10
R-HSA-69618 5.135524e-11 1.364337e-08 1.223516e-08
R-HSA-2500257 1.006794e-10 2.006036e-08 1.798981e-08
R-HSA-141424 1.923239e-10 2.554702e-08 2.291016e-08
R-HSA-141444 1.923239e-10 2.554702e-08 2.291016e-08
geneID
R-HSA-69278 CDC45/CDCA8/CDC20/FOXM1/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/RRM2/UBE2C/HJURP/SKA1/TPX2/NEK2/CENPM/CENPN/UBE2S/CCNA2/CDK1/ERCC6L/GINS1/KIF18A/CDT1/NCAPG/AURKB/GINS2/KIF20A/AURKA/CCNB1/MCM5/PTTG1/MCM2/KIF2C/CDC25A/CDC6/PLK1/BUB1B/GTSE1/ZWINT/SPC25/CENPI/ESPL1/TK1/CCNE1/ORC6/ORC1/TAOK1
R-HSA-69620 CDC45/CDCA8/CDC20/CENPE/CCNB2/NDC80/UBE2C/SKA1/CENPM/CENPN/UBE2S/CCNA2/CDK1/ERCC6L/KIF18A/AURKB/CHEK1/CCNB1/MCM5/MCM2/KIF2C/CDC25A/CDC6/PLK1/BUB1B/GTSE1/ZWINT/SPC25/CENPI/CCNE1/ORC6/ORC1/TAOK1
R-HSA-69618 CDCA8/CDC20/CENPE/NDC80/UBE2C/SKA1/CENPM/CENPN/UBE2S/ERCC6L/KIF18A/AURKB/KIF2C/PLK1/BUB1B/ZWINT/SPC25/CENPI/TAOK1
R-HSA-2500257 CDCA8/CDC20/CENPE/CCNB2/NDC80/SKA1/CENPM/CENPN/CDK1/ERCC6L/KIF18A/AURKB/CCNB1/KIF2C/PLK1/BUB1B/ZWINT/SPC25/CENPI/TAOK1
R-HSA-141424 CDCA8/CDC20/CENPE/NDC80/SKA1/CENPM/CENPN/ERCC6L/KIF18A/AURKB/KIF2C/PLK1/BUB1B/ZWINT/SPC25/CENPI/TAOK1
R-HSA-141444 CDCA8/CDC20/CENPE/NDC80/SKA1/CENPM/CENPN/ERCC6L/KIF18A/AURKB/KIF2C/PLK1/BUB1B/ZWINT/SPC25/CENPI/TAOK1
Count
R-HSA-69278 49
R-HSA-69620 33
R-HSA-69618 19
R-HSA-2500257 20
R-HSA-141424 17
R-HSA-141444 17
Reactome pathway gene set enrichment analysis
y <- gsePathway ( geneList , pvalueCutoff = 0.2 ,
pAdjustMethod = "BH" ,
verbose = FALSE )
head ( y )
ID Description setSize
R-HSA-69278 R-HSA-69278 Cell Cycle, Mitotic 382
R-HSA-453279 R-HSA-453279 Mitotic G1 phase and G1/S transition 113
R-HSA-69620 R-HSA-69620 Cell Cycle Checkpoints 194
R-HSA-69206 R-HSA-69206 G1/S Transition 100
R-HSA-69239 R-HSA-69239 Synthesis of DNA 89
R-HSA-1640170 R-HSA-1640170 Cell Cycle 473
enrichmentScore NES pvalue p.adjust qvalue rank
R-HSA-69278 0.6235874 3.011407 1e-10 4.751613e-09 3.470289e-09 1769
R-HSA-453279 0.7235270 2.973793 1e-10 4.751613e-09 3.470289e-09 1155
R-HSA-69620 0.6662086 2.973144 1e-10 4.751613e-09 3.470289e-09 1768
R-HSA-69206 0.7204590 2.911921 1e-10 4.751613e-09 3.470289e-09 1155
R-HSA-69239 0.7294921 2.904831 1e-10 4.751613e-09 3.470289e-09 1769
R-HSA-1640170 0.5850735 2.884988 1e-10 4.751613e-09 3.470289e-09 1769
leading_edge
R-HSA-69278 tags=38%, list=14%, signal=34%
R-HSA-453279 tags=44%, list=9%, signal=41%
R-HSA-69620 tags=42%, list=14%, signal=36%
R-HSA-69206 tags=45%, list=9%, signal=41%
R-HSA-69239 tags=55%, list=14%, signal=48%
R-HSA-1640170 tags=34%, list=14%, signal=31%
core_enrichment
R-HSA-69278 8318/55143/991/2305/1062/4605/9133/10403/7153/23397/6241/11065/55355/220134/22974/4751/79019/55839/27338/890/983/54821/9837/81930/81620/64151/9212/51659/10112/6790/891/4174/9232/4171/11004/993/990/5347/701/51512/11130/57405/2491/9700/7083/898/23594/4998/10733/1163/54801/9134/4175/4173/2237/5984/994/9918/7298/84296/699/4609/1063/85236/5111/28227/9688/64785/5709/26271/55055/51053/1869/1029/1763/1719/8970/54892/8357/5693/8317/7277/5427/23649/7112/5713/3930/79980/9735/55732/11047/5557/23310/5691/1871/1031/80086/995/10051/1104/5685/84790/1019/5558/4172/9631/5424/79866/5690/5885/5686/5695/203068/7027/10213/1875/23175/8345/7283/10381/5983/7979/54908/10592/23165/10383/3018/22822/5714/10376/7443/55706/8815/5702/3014/1030/23636/9978/5905/5425/5708/55166/5692/10393/54107
R-HSA-453279 8318/4605/7153/6241/890/983/81620/891/4174/4171/993/990/7083/898/23594/4998/1163/9134/4175/4173/7298/4609/5111/28227/5709/26271/51053/1869/1029/1719/5693/8317/5427/23649/5713/11047/5557/5691/1871/1031/5685/1019/5558/4172/5690/5686/5695/7027/10213/1875
R-HSA-69620 8318/55143/991/1062/9133/10403/11065/220134/79019/55839/27338/890/983/54821/81930/9212/1111/891/4174/4171/11004/993/990/5347/701/51512/11130/57405/2491/898/23594/4998/9134/4175/4173/5984/699/1063/85236/5709/55055/641/1029/1763/8970/5693/8317/5713/79980/9735/11047/2810/5691/995/5685/4172/7336/5690/83990/5686/5695/11200/10213/8345/7534/80010/5983/7979/54908/4683/63967/3018/5714/5702/3014/9978/5905/5708/55166/5692/10393
R-HSA-69206 8318/6241/890/983/81620/891/4174/4171/993/990/7083/898/23594/4998/1163/9134/4175/4173/7298/4609/5111/28227/5709/26271/51053/1869/1719/5693/8317/5427/23649/5713/11047/5557/5691/5685/1019/5558/4172/5690/5686/5695/7027/10213/1875
R-HSA-69239 8318/11065/27338/890/9837/81620/51659/4174/4171/990/898/23594/4998/9134/4175/4173/2237/5984/84296/5111/64785/5709/51053/1763/5693/5427/23649/5713/11047/5557/5691/5685/5558/4172/5424/5690/5686/5695/10213/5983/7979/5714/5702/9978/5425/5708/5692/10393/54107
R-HSA-1640170 8318/55143/991/2305/1062/4605/9133/10403/7153/23397/6241/11065/55355/220134/22974/4751/79019/55839/27338/890/983/54821/9837/81930/81620/64151/9212/51659/1111/10112/6790/891/4174/9232/4171/11004/993/990/5347/701/51512/11130/57405/79075/2491/9700/7083/898/23594/4998/11339/10733/1163/54801/9134/4175/4173/2237/5984/994/9918/7298/84296/699/4609/1063/85236/5111/28227/9688/64785/5709/26271/55055/51053/641/1869/1029/1763/1719/8970/54892/8357/5693/8317/7277/5427/23649/7112/5713/3930/79980/5435/9735/55732/11047/5557/2810/23310/5691/1871/1031/8607/80086/995/10051/1104/5685/84790/1019/5558/4172/9631/5424/79866/7336/5690/83990/5885/5686/5695/11200/203068/7027/10213/1875/23175/8345/7534/7283/80010/10381/5983/5440/7979/54908/10592/4683/54069/23165/10383/63967/3018/22822/5714/10376/7443/55706/8815/5702/3014/1030/23636/9978/5905/5425/5708/55166/5692/5433/10393/54107
Pathway Visualization
ReactomePA implemented the viewPathway() enrichplot package and are documented in Chapter 13
(ref:viewpathwayscap) Visualize reactome pathway.
(ref:viewpathwaycap) Visualize reactome pathway.
viewPathway ( "E2F mediated regulation of DNA replication" , readable = TRUE ,
foldChange = geneList )
References
Yu, Guangchuang, and Qing-Yu He. 2016.
“ReactomePA : An r/Bioconductor Package for Reactome Pathway Analysis and Visualization.” Molecular BioSystems 12 (2): 477–79.
https://doi.org/10.1039/C5MB00663E .
