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() that uses hypergeometric model to assess whether the number of selected genes associated with a reactome pathway is larger than expected.
library (ReactomePA)data (geneList, package= "DOSE" <- names (geneList)[abs (geneList) > 1.5 ]head (de)
[1] "4312" "8318" "10874" "55143" "55388" "991"
<- enrichPathway (gene= de, pvalueCutoff = 0.05 , readable= TRUE )head (x)
ID
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
R-HSA-68882 R-HSA-68882
Description
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
R-HSA-68882 Mitotic Anaphase
GeneRatio BgRatio RichFactor FoldEnrichment oddsRatio zScore
R-HSA-69620 38/342 292/11287 0.1301370 4.294901 5.261319 10.083502
R-HSA-69618 22/342 113/11287 0.1946903 6.425348 8.200137 10.245607
R-HSA-2500257 23/342 129/11287 0.1782946 5.884242 7.372597 9.862206
R-HSA-141424 20/342 96/11287 0.2083333 6.875609 8.882805 10.219491
R-HSA-141444 20/342 96/11287 0.2083333 6.875609 8.882805 10.219491
R-HSA-68882 28/342 225/11287 0.1244444 4.107031 4.865078 8.321376
pvalue p.adjust qvalue
R-HSA-69620 1.988463e-14 1.805524e-11 1.805524e-11
R-HSA-69618 2.386464e-12 1.083455e-09 1.083455e-09
R-HSA-2500257 5.135365e-12 1.182511e-09 1.182511e-09
R-HSA-141424 6.511625e-12 1.182511e-09 1.182511e-09
R-HSA-141444 6.511625e-12 1.182511e-09 1.182511e-09
R-HSA-68882 1.865374e-10 2.686794e-08 2.686794e-08
geneID
R-HSA-69620 UBE2S/MCM2/ORC1/CDK1/BIRC5/CDC20/CDC6/SPC25/CDCA8/MCM5/ORC6/CENPI/KIF2C/AURKB/MCM10/CDC45/CCNE1/CCNB1/CCNA2/UBE2C/CENPN/ERCC6L/BUB1B/CDC25A/GTSE1/KIF18A/CENPE/TAOK1/SKA1/ZWINT/EXO1/CHEK1/PLK1/NDC80/CENPM/CCNB2/MAD2L1/CENPU
R-HSA-69618 UBE2S/BIRC5/CDC20/SPC25/CDCA8/CENPI/KIF2C/AURKB/UBE2C/CENPN/ERCC6L/BUB1B/KIF18A/CENPE/TAOK1/SKA1/ZWINT/PLK1/NDC80/CENPM/MAD2L1/CENPU
R-HSA-2500257 CDK1/BIRC5/CDC20/SPC25/CDCA8/CENPI/KIF2C/AURKB/CCNB1/CENPN/ERCC6L/BUB1B/KIF18A/CENPE/TAOK1/SKA1/ZWINT/PLK1/NDC80/CENPM/CCNB2/MAD2L1/CENPU
R-HSA-141424 BIRC5/CDC20/SPC25/CDCA8/CENPI/KIF2C/AURKB/CENPN/ERCC6L/BUB1B/KIF18A/CENPE/TAOK1/SKA1/ZWINT/PLK1/NDC80/CENPM/MAD2L1/CENPU
R-HSA-141444 BIRC5/CDC20/SPC25/CDCA8/CENPI/KIF2C/AURKB/CENPN/ERCC6L/BUB1B/KIF18A/CENPE/TAOK1/SKA1/ZWINT/PLK1/NDC80/CENPM/MAD2L1/CENPU
R-HSA-68882 UBE2S/PTTG1/CDK1/BIRC5/CDC20/SPC25/CDCA8/CENPI/KIF2C/AURKB/CCNB1/LMNB1/UBE2C/CENPN/ERCC6L/BUB1B/KIF18A/CENPE/TAOK1/SKA1/ZWINT/PLK1/NDC80/CENPM/ESPL1/CCNB2/MAD2L1/CENPU
Count
R-HSA-69620 38
R-HSA-69618 22
R-HSA-2500257 23
R-HSA-141424 20
R-HSA-141444 20
R-HSA-68882 28
Reactome pathway gene set enrichment analysis
<- gsePathway (geneList, pvalueCutoff = 0.2 ,pAdjustMethod = "BH" , verbose = FALSE )head (y)
ID Description setSize
R-HSA-453279 R-HSA-453279 Mitotic G1 phase and G1/S transition 132
R-HSA-69206 R-HSA-69206 G1/S Transition 114
R-HSA-69620 R-HSA-69620 Cell Cycle Checkpoints 238
R-HSA-69278 R-HSA-69278 Cell Cycle, Mitotic 451
R-HSA-2555396 R-HSA-2555396 Mitotic Metaphase and Anaphase 190
R-HSA-69239 R-HSA-69239 Synthesis of DNA 99
enrichmentScore NES pvalue p.adjust qvalue rank
R-HSA-453279 0.7117138 3.065288 1e-10 4.648571e-09 4.648571e-09 1155
R-HSA-69206 0.7163844 3.009853 1e-10 4.648571e-09 4.648571e-09 1155
R-HSA-69620 0.6508576 2.987239 1e-10 4.648571e-09 4.648571e-09 1905
R-HSA-69278 0.6094048 2.970349 1e-10 4.648571e-09 4.648571e-09 1769
R-HSA-2555396 0.6536752 2.960902 1e-10 4.648571e-09 4.648571e-09 1857
R-HSA-69239 0.7192759 2.959526 1e-10 4.648571e-09 4.648571e-09 1905
leading_edge
R-HSA-453279 tags=43%, list=9%, signal=40%
R-HSA-69206 tags=45%, list=9%, signal=41%
R-HSA-69620 tags=42%, list=15%, signal=36%
R-HSA-69278 tags=36%, list=14%, signal=32%
R-HSA-2555396 tags=41%, list=15%, signal=35%
R-HSA-69239 tags=57%, list=15%, signal=48%
core_enrichment
R-HSA-453279 8318/55388/4605/7153/6241/890/983/81620/891/4174/4171/993/990/7083/898/23594/4998/1163/9134/4175/4173/10926/6502/7298/4609/5111/28227/5688/5709/26271/51053/1869/1029/1719/4067/5693/8317/5427/23649/4176/5713/11047/5557/5691/1871/1031/5685/1019/5558/4172/5690/5684/5686/5695/7027/10213/1875
R-HSA-69206 8318/55388/6241/890/983/81620/891/4174/4171/993/990/7083/898/23594/4998/1163/9134/4175/4173/10926/6502/7298/4609/5111/28227/5688/5709/26271/51053/1869/1719/5693/8317/5427/23649/4176/5713/11047/5557/5691/5685/1019/5558/4172/5690/5684/5686/5695/7027/10213/1875
R-HSA-69620 8318/55143/55388/991/1062/9133/10403/11065/220134/79019/55839/27338/890/983/54821/4085/81930/332/9212/1111/891/4174/4171/11004/993/990/5347/701/51512/9156/11130/79682/57405/2491/898/23594/4998/9134/4175/4173/10926/5984/1058/699/1063/85236/5688/5709/55055/641/1029/1763/8970/5693/8317/4176/5713/79980/5982/9735/11047/2810/5691/9088/995/5685/7468/4172/7336/5690/5684/83990/5686/5695/11200/10213/8345/7534/80010/5983/7979/54908/6396/4683/63967/3018/5714/5702/3014/9978/5905/3619/5708/55166/5692/10393/8290/5704/580/6119
R-HSA-69278 8318/55143/55388/991/2305/9493/1062/4605/9133/10403/7153/23397/6241/11065/55355/220134/22974/4751/79019/55839/27338/890/983/54821/4085/9837/81930/81620/332/64151/9212/51659/10112/6790/891/4174/9232/4001/4171/3161/11004/993/990/5347/701/51512/11130/79682/57405/2491/9700/7083/898/23594/4998/10733/1163/54801/9134/4175/4173/2237/10926/6502/5984/994/9918/7298/1058/84296/699/4609/1063/85236/5111/28227/5688/9688/64785/5709/26271/55055/51053/1869/1029/1763/1719/8970/54892/8357/4067/5693/8317/7277/5427/23649/4176/7112/5713/3930/79980/5982/9735/55732/11047/5557/23310/5691/1871/1031/80086/9088/995/10051/1104/5685/84790/1019/5558/4172/9631/5424/7444/79866/5690/5684/5885/5686/5695/203068/7027/10213/1875/23175/8345/7283/10381/5983/7979/54908/10592/6396/23165/10383/3018/22822/5714/10376/7443/55706/8815/5702/3014/1030/23636/9978/5905/3619/5425/5708/55166/5692/10393/54107
R-HSA-2555396 55143/991/1062/9133/10403/11065/220134/79019/55839/27338/983/54821/4085/81930/332/9212/891/9232/4001/11004/5347/701/11130/79682/57405/2491/9700/1058/699/1063/5688/9688/5709/26271/55055/5693/7277/7112/5713/3930/79980/9735/11047/5691/80086/1104/5685/84790/9631/7444/5690/5684/5885/5686/5695/10213/10381/7979/54908/6396/23165/10383/5714/10376/7443/55706/8815/5702/23636/5905/3619/5708/55166/5692/10393/5704/5901
R-HSA-69239 8318/11065/27338/890/9837/81620/51659/4174/4171/990/898/23594/4998/9134/4175/4173/2237/6502/5984/84296/5111/5688/64785/5709/51053/1763/5693/5427/23649/4176/5713/5982/11047/5557/5691/5685/5558/4172/5424/5690/5684/5686/5695/10213/5983/7979/5714/5702/9978/5425/5708/5692/10393/54107/5704/6119
log2err
R-HSA-453279 NaN
R-HSA-69206 NaN
R-HSA-69620 NaN
R-HSA-69278 NaN
R-HSA-2555396 NaN
R-HSA-69239 NaN
Pathway Visualization
ReactomePA implemented the viewPathway() to visualize selected reactome pathways. More general purpose visualization methods for ORA and GSEA results are provided in the enrichplot package and are documented in Chapter 14 Figure 8.1 for an example.
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 .
