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-9648025 R-HSA-9648025
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-9648025 EML4 and NUDC in mitotic spindle formation
GeneRatio BgRatio RichFactor FoldEnrichment zScore
R-HSA-69620 38/340 292/11230 0.1301370 4.298348 10.090554
R-HSA-69618 22/340 113/11230 0.1946903 6.430505 10.251365
R-HSA-2500257 23/340 129/11230 0.1782946 5.888965 9.867946
R-HSA-141424 20/340 96/11230 0.2083333 6.881127 10.225079
R-HSA-141444 20/340 96/11230 0.2083333 6.881127 10.225079
R-HSA-9648025 20/340 119/11230 0.1680672 5.551162 8.818916
pvalue p.adjust qvalue
R-HSA-69620 1.923682e-14 3.256793e-11 3.256793e-11
R-HSA-69618 2.342233e-12 1.982700e-09 1.982700e-09
R-HSA-2500257 5.036854e-12 2.167812e-09 2.167812e-09
R-HSA-141424 6.402279e-12 2.167812e-09 2.167812e-09
R-HSA-141444 6.402279e-12 2.167812e-09 2.167812e-09
R-HSA-9648025 3.854310e-10 1.087558e-07 1.087558e-07
geneID
R-HSA-69620 CCNB1/UBE2C/MCM2/UBE2S/CENPE/TAOK1/CDK1/SKA1/CENPI/KIF18A/EXO1/CDC20/CDC6/ERCC6L/MCM5/CCNB2/BUB1B/AURKB/CCNA2/PLK1/ORC1/ZWINT/CDC45/CHEK1/CENPM/NDC80/SPC25/GTSE1/KIF2C/MCM10/ORC6/CDC25A/CENPN/BIRC5/CDCA8/CENPU/MAD2L1/CCNE1
R-HSA-69618 UBE2C/UBE2S/CENPE/TAOK1/SKA1/CENPI/KIF18A/CDC20/ERCC6L/BUB1B/AURKB/PLK1/ZWINT/CENPM/NDC80/SPC25/KIF2C/CENPN/BIRC5/CDCA8/CENPU/MAD2L1
R-HSA-2500257 CCNB1/CENPE/TAOK1/CDK1/SKA1/CENPI/KIF18A/CDC20/ERCC6L/CCNB2/BUB1B/AURKB/PLK1/ZWINT/CENPM/NDC80/SPC25/KIF2C/CENPN/BIRC5/CDCA8/CENPU/MAD2L1
R-HSA-141424 CENPE/TAOK1/SKA1/CENPI/KIF18A/CDC20/ERCC6L/BUB1B/AURKB/PLK1/ZWINT/CENPM/NDC80/SPC25/KIF2C/CENPN/BIRC5/CDCA8/CENPU/MAD2L1
R-HSA-141444 CENPE/TAOK1/SKA1/CENPI/KIF18A/CDC20/ERCC6L/BUB1B/AURKB/PLK1/ZWINT/CENPM/NDC80/SPC25/KIF2C/CENPN/BIRC5/CDCA8/CENPU/MAD2L1
R-HSA-9648025 CENPE/TAOK1/SKA1/CENPI/KIF18A/CDC20/ERCC6L/BUB1B/AURKB/PLK1/ZWINT/CENPM/NDC80/SPC25/KIF2C/CENPN/BIRC5/CDCA8/CENPU/MAD2L1
Count
R-HSA-69620 38
R-HSA-69618 22
R-HSA-2500257 23
R-HSA-141424 20
R-HSA-141444 20
R-HSA-9648025 20
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-69239 R-HSA-69239 Synthesis of DNA 99
R-HSA-69206 R-HSA-69206 G1/S Transition 114
R-HSA-69481 R-HSA-69481 G2/M Checkpoints 125
enrichmentScore NES pvalue p.adjust qvalue
R-HSA-453279 0.7117138 3.048939 3.068716e-12 2.502273e-10 2.502273e-10
R-HSA-69620 0.6508575 2.997741 3.963758e-12 2.581016e-10 2.581016e-10
R-HSA-69306 0.6877315 2.951697 3.364733e-12 2.502273e-10 2.502273e-10
R-HSA-69239 0.7192759 2.939280 2.998373e-12 2.502273e-10 2.502273e-10
R-HSA-69206 0.7163844 2.926437 3.408573e-12 2.502273e-10 2.502273e-10
R-HSA-69481 0.6968898 2.897815 3.453571e-12 2.502273e-10 2.502273e-10
rank leading_edge
R-HSA-453279 1155 tags=43%, list=9%, signal=40%
R-HSA-69620 1905 tags=42%, list=15%, signal=36%
R-HSA-69306 1769 tags=47%, list=14%, signal=41%
R-HSA-69239 1905 tags=57%, list=15%, signal=48%
R-HSA-69206 1155 tags=45%, list=9%, signal=41%
R-HSA-69481 1905 tags=50%, list=15%, signal=43%
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-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
R-HSA-69481 8318/55388/9133/890/983/1111/891/4174/4171/993/990/51512/9156/23594/4998/4175/4173/10926/5984/85236/5688/5709/641/1763/8970/5693/8317/4176/5713/5982/11047/2810/5691/9088/995/5685/7468/4172/7336/5690/5684/83990/5686/5695/11200/10213/8345/7534/80010/5983/7979/4683/63967/3018/5714/5702/3014/5708/5692/8290/5704/580/6119
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
(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 .
