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 zScore
R-HSA-69620 38/342 292/11287 0.1301370 4.294901 10.083502
R-HSA-69618 22/342 113/11287 0.1946903 6.425348 10.245607
R-HSA-2500257 23/342 129/11287 0.1782946 5.884242 9.862206
R-HSA-141424 20/342 96/11287 0.2083333 6.875609 10.219491
R-HSA-141444 20/342 96/11287 0.2083333 6.875609 10.219491
R-HSA-68882 28/342 225/11287 0.1244444 4.107031 8.321376
pvalue p.adjust qvalue
R-HSA-69620 1.988463e-14 3.428110e-11 3.428110e-11
R-HSA-69618 2.386464e-12 2.057132e-09 2.057132e-09
R-HSA-2500257 5.135365e-12 2.245208e-09 2.245208e-09
R-HSA-141424 6.511625e-12 2.245208e-09 2.245208e-09
R-HSA-141444 6.511625e-12 2.245208e-09 2.245208e-09
R-HSA-68882 1.865374e-10 5.101358e-08 5.101358e-08
geneID
R-HSA-69620 AURKB/CCNB1/CENPI/ZWINT/CDCA8/UBE2S/PLK1/CDK1/CDC6/KIF2C/EXO1/UBE2C/CHEK1/CDC20/GTSE1/MCM5/CENPU/MAD2L1/BIRC5/CDC45/SPC25/CDC25A/BUB1B/ORC1/CENPE/TAOK1/KIF18A/CCNB2/ERCC6L/MCM10/CCNA2/CENPN/CCNE1/NDC80/CENPM/MCM2/ORC6/SKA1
R-HSA-69618 AURKB/CENPI/ZWINT/CDCA8/UBE2S/PLK1/KIF2C/UBE2C/CDC20/CENPU/MAD2L1/BIRC5/SPC25/BUB1B/CENPE/TAOK1/KIF18A/ERCC6L/CENPN/NDC80/CENPM/SKA1
R-HSA-2500257 AURKB/CCNB1/CENPI/ZWINT/CDCA8/PLK1/CDK1/KIF2C/CDC20/CENPU/MAD2L1/BIRC5/SPC25/BUB1B/CENPE/TAOK1/KIF18A/CCNB2/ERCC6L/CENPN/NDC80/CENPM/SKA1
R-HSA-141424 AURKB/CENPI/ZWINT/CDCA8/PLK1/KIF2C/CDC20/CENPU/MAD2L1/BIRC5/SPC25/BUB1B/CENPE/TAOK1/KIF18A/ERCC6L/CENPN/NDC80/CENPM/SKA1
R-HSA-141444 AURKB/CENPI/ZWINT/CDCA8/PLK1/KIF2C/CDC20/CENPU/MAD2L1/BIRC5/SPC25/BUB1B/CENPE/TAOK1/KIF18A/ERCC6L/CENPN/NDC80/CENPM/SKA1
R-HSA-68882 AURKB/CCNB1/LMNB1/CENPI/ZWINT/CDCA8/UBE2S/PLK1/CDK1/KIF2C/UBE2C/CDC20/PTTG1/CENPU/MAD2L1/BIRC5/SPC25/BUB1B/CENPE/TAOK1/KIF18A/CCNB2/ERCC6L/CENPN/ESPL1/NDC80/CENPM/SKA1
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-69620 R-HSA-69620 Cell Cycle Checkpoints 238
R-HSA-69306 R-HSA-69306 DNA Replication 133
R-HSA-68882 R-HSA-68882 Mitotic Anaphase 189
R-HSA-69239 R-HSA-69239 Synthesis of DNA 99
R-HSA-69206 R-HSA-69206 G1/S Transition 114
enrichmentScore NES pvalue p.adjust qvalue rank
R-HSA-453279 0.7117138 3.011407 1e-10 5.746667e-09 5.746667e-09 1155
R-HSA-69620 0.6508575 2.975031 1e-10 5.746667e-09 5.746667e-09 1905
R-HSA-69306 0.6877315 2.953795 1e-10 5.746667e-09 5.746667e-09 1769
R-HSA-68882 0.6518659 2.944869 1e-10 5.746667e-09 5.746667e-09 1857
R-HSA-69239 0.7192759 2.906679 1e-10 5.746667e-09 5.746667e-09 1905
R-HSA-69206 0.7163844 2.898739 1e-10 5.746667e-09 5.746667e-09 1155
leading_edge
R-HSA-453279 tags=43%, list=9%, signal=40%
R-HSA-69620 tags=42%, list=15%, signal=36%
R-HSA-69306 tags=47%, list=14%, signal=41%
R-HSA-68882 tags=40%, list=15%, signal=35%
R-HSA-69239 tags=57%, list=15%, signal=48%
R-HSA-69206 tags=45%, list=9%, signal=41%
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-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-69306 8318/55388/11065/27338/890/9837/81620/51659/4174/4171/990/898/23594/4998/9134/4175/4173/2237/10926/6502/5984/84296/85236/5111/5688/64785/5709/51053/1763/8970/8357/5693/8317/5427/23649/4176/5713/5982/11047/5557/5691/5685/5558/4172/5424/5690/5684/5686/5695/10213/8345/5983/7979/3018/5714/5702/3014/9978/5425/5708/5692/10393/54107
R-HSA-68882 55143/991/1062/9133/10403/11065/220134/79019/55839/27338/983/54821/4085/81930/332/9212/891/9232/4001/11004/5347/701/11130/79682/57405/2491/9700/1058/699/1063/5688/9688/5709/55055/5693/7277/7112/5713/3930/79980/9735/11047/5691/80086/1104/5685/84790/9631/7444/5690/5684/5885/5686/5695/10213/10381/7979/54908/6396/23165/10383/5714/10376/7443/55706/8815/5702/23636/5905/3619/5708/55166/5692/10393/5704/5901
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
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
log2err
R-HSA-453279 NaN
R-HSA-69620 NaN
R-HSA-69306 NaN
R-HSA-68882 NaN
R-HSA-69239 NaN
R-HSA-69206 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 13 Figure 7.1 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 .
