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EntrezGene ID GeneName
51703 ACSL5
94 ACVRL1
211 ALAS1
23092 ARHGAP26
9459 ARHGEF6
55589 BMP2K
1234 CCR5
253175 CDY1
9085 CDY1
203611 CDY1
9426 CDY1
253175 CDY1B
9085 CDY1B
203611 CDY1B
9426 CDY1B
203611 CDY2A
9426 CDY2A
253175 CDY2A
9085 CDY2A
203611 CDY2B
9426 CDY2B
253175 CDY2B
9085 CDY2B
9620 CELSR1
101928723 CHD5
26038 CHD5
1131 CHRM3
1138 CHRNA5
1259 CNGA1
10699 CORIN
1359 CPA3
1472 CST4
10800 CYSLTR1
2191 FAP
2213 FCGR2B
54328 GPR173
338442 HCAR2
57657 HCN3
9146 HGS
8518 IKBKAP
3559 IL2RA
10994 ILVBL
3619 INCENP
10788 IQGAP2
3704 ITPA
4058 LTK
4063 LY9
4216 MAP3K4
5871 MAP4K2
4593 MUSK
83463 MXD3
91807 MYLK3
8386 OR1D5
5122 PCSK1
5833 PCYT2
5142 PDE4B
5213 PFKM
11284 PNKP
5430 POLR2A
5510 PPP1R7
5523 PPP2R3A
5531 PPP4C
5538 PPT1
85481 PSKH2
11251 PTGDR2
10076 PTPRU
25945 PVRL3
51762 RAB8B
64080 RBKS
8607 RUVBL1
122042 RXFP2
89777 SERPINB12
6494 SIPA1
8877 SPHK1
7980 TFPI2
112858 TP53RK
7179 TPTE
51175 TUBE1
5756 TWF1
UniProt cluster
A0A087WPR9 1
A0A0A6YY91 1
A1L332 1
A2A9X5 1
A2AGS2 1
A2AGS6 1
A2AM29 1
A3KG01 1
A3KGE4 1
B1AS34 1
B1AV01 1
B1AWZ5 1
B2RWX4 1
C9K0Z6 1
D3Z0V7 1
E2QRQ3 1
E9PWE8 1
E9Q6Q2 1
E9Q8X9 1
E9QMD3 1
E9QN14 1
E9QNZ2 1
F2Z470 1
F7BGR7 1
F7C528 1
F8WGN6 1
G3X9L6 1
H3BLR1 1
J3JRU4 1
O08553 1
O08599 1
O35098 1
O54879 1
O55126 1
P08551 1
P12025 1
P20152 1
P20357 1
P22935 1
P28738 1
P45591 1
P46660 1
P61264 1
Q00915 1
Q14AX3 1
Q14DQ3 1
Q3TEA8 1
Q3TRK3 1
Q3TVU9 1
Q3TWM9 1
Q3U8W9 1
Q3UID0 1
Q3UWS9 1
Q3UZJ4 1
Q5DTK0 1
Q5SQX6 1
Q61301 1
Q64511 1
Q66JR8 1
Q6A051 1
Q6GR78 1
Q6NZL0 1
Q6PDL0 1
Q6R891 1
Q78IK4 1
Q80YA7 1
Q8BJS4 1
Q8BP00 1
Q8BUK6 1
Q8C1Y3 1
Q8CCK0 1
Q8CDZ6 1
Q8K394 1
Q8K3C3 1
Q8R572 1
Q8VBT0 1
Q8VCW8 1
Q8VDP4 1
Q8VEH3 1
Q91XV3 1
Q922J3 1
Q99KJ8 1
Q9BCZ4 1
Q9CQ54 1
Q9CZC8 1
Q9D394 1
Q9D5H8 1
Q9D8S3 1
Q9DCJ5 1
Q9EQF6 1
Q9JJV2 1
Q9JKN6 1
Q9JLZ3 1
Q9JMG7 1
Q9QYS9 1
Q9QZM4 1
Q9R226 1
Q9WUL7 1
A0JLN6 2
A2TJV2 2
A8CA96 2
A8Y5N8 2
B2RX07 2
D0VLQ4 2
D3Z112 2
D3Z3H0 2
E3WH30 2
E9PV84 2
E9Q391 2
E9Q616 2
E9Q6S4 2
E9Q7E5 2
E9Q8D0 2
F6VY18 2
F6Y247 2
F8WIT2 2
G3UYN0 2
G5E8P4 2
H7BX50 2
J7I1C3 2
O35488 2
O88735 2
P02798 2
P08226 2
P14602 2
P24472 2
P48678 2
P56371 2
P58242 2
P59178 2
P68368 2
P70700 2
P97384 2
Q03145 2
Q07133 2
Q3TA91 2
Q3TIJ5 2
Q3TLA8 2
Q3U0X6 2
Q3U202 2
Q3U3X7 2
Q3UGF9 2
Q3UKP5 2
Q3V492 2
Q4V9T7 2
Q5FWJ5 2
Q5SSZ5 2
Q61539 2
Q62315 2
Q69ZR9 2
Q6GU23 2
Q6IE82 2
Q6NSQ7 2
Q6QMT3 2
Q6ZPI0 2
Q6ZQL4 2
Q7TN89 2
Q7TSZ8 2
Q80UY2 2
Q80VR2 2
Q8BLG0 2
Q8C6P8 2
Q8CD92 2
Q8CGZ0 2
Q8CIB9 2
Q8K403 2
Q8K4R9 2
Q8R0F5 2
Q8R0K9 2
Q8R0W0 2
Q8R2Q8 2
Q8R3C6 2
Q8R409 2
Q8VCF1 2
Q8VCN5 2
Q91XC0 2
Q91YU8 2
Q921M7 2
Q99JX6 2
Q99PB4 2
Q9CWR8 2
Q9CYX7 2
Q9D6D9 2
Q9EQK5 2
Q9JJ66 2
Q9QUR4 2
Q9QYY0 2
Q9R069 2
Q9R0X4 2
Q9Z0P5 2
A2AFW6 3
A2AKX3 3
A2ATU0 3
A6H605 3
A6PWY4 3
B2RRE4 3
B2RRE7 3
B2ZRS8 3
B9EJX5 3
D3YVL0 3
D3YVU7 3
E9PUB0 3
E9QN31 3
F8VQJ3 3
G3UXN4 3
G3X8Q0 3
G3X9B1 3
O08901 3
O09130 3
O54946 3
O70445 3
O88792 3
P04184 3
P05064 3
P10852 3
P23492 3
P29351 3
P51432 3
P62911 3
P70278 3
P97329 3
Q04692 3
Q0VGV0 3
Q3TLD5 3
Q3TQZ0 3
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Q3U2S8 3
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Q3UH06 3
Q3UH94 3
Q3UHX9 3
Q3UIL6 3
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Q5SFM8 3
Q5SWD9 3
Q60848 3
Q61792 3
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Q6P5B0 3
Q6PFE3 3
Q6ZPR6 3
Q75N73 3
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Q8BGA5 3
Q8BGS0 3
Q8BHX3 3
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Q8BKG3 3
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Q8K298 3
Q8K2C1 3
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Q8R3N1 3
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Q8VDF2 3
Q8VEE4 3
Q91WA1 3
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Q925B0 3
Q99KR3 3
Q99KV5 3
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Q9CR57 3
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Q9CXX1 3
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Q9D297 3
Q9DBC7 3
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A0A087WNZ7 4
A2ARV4 4
A2AW86 4
D3YW26 4
D3YWX2 4
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A0A068BGR9 5
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A0A0A0MQD2 5
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K3W4L0 5
O08738 5
O55127 5
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O55222 5
O70480 5
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P05532 5
P06837 5
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P10833 5
P12265 5
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#---------------------------------------------------------------------------------------
# Exercise 2
#---------------------------------------------------------------------------------------
# Given a list of hits and a background in folder /Exercise 2
# background.txt and id_list.txt
# perform enrichment analysis against
# 1. Gene Ontology,
# 2. Kegg modules, and
# 3. DisGeNet (diseases)
# For each result produce a cnetplot and an upsetplot.
# - you will need to provide the correct id's for the functions to execute - use converters
# - vary the p-value q-value thresholds in case of an empty result
# - make the disgenet output readable (gene names, not entrez id's)
background <- read.csv("/Users/rogon/Work/01. Teaching/CBNA Courses/2020 Online Course Series/2020 CBNA-DeNBI Enrichment course - my materials/Part 2 - R-code session ClusterProfiler, ReactomePA, pathfindR/Exercise 2 (custom background)/Background.txt", sep="")
id_list <- read.delim("/Users/rogon/Work/01. Teaching/CBNA Courses/2020 Online Course Series/2020 CBNA-DeNBI Enrichment course - my materials/Part 2 - R-code session ClusterProfiler, ReactomePA, pathfindR/Exercise 2 (custom background)/id_list.txt")
keytypes(org.Hs.eg.db)
entrez_map <- bitr(background$GeneID, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Hs.eg.db", drop= FALSE)
# or biomart:
# you will need to convert identifiers - for that purpose I suggest using the biomaRt package in R, alternatively you can use the website itselt
# ensembl biomart http://www.ensembl.org/biomart/martview/
library("biomaRt")
ensembl = biomaRt::useMart("ensembl")
ensembl = useDataset("hsapiens_gene_ensembl", mart=ensembl)
datasets_biomart <- listDatasets(ensembl)
attributes_biomart <- listAttributes(ensembl)
id_list_biomart= getBM(attributes = c("hgnc_symbol","entrezgene_id", "ensembl_gene_id"),
filters = c(filters = "entrezgene_id"),
values = id_list$EntrezGene.ID,
mart = ensembl)
background_biomart= getBM(attributes = c("hgnc_symbol","entrezgene_id", "ensembl_gene_id"),
filters = c(filters = "hgnc_symbol"),
values = background$GeneID,
mart = ensembl)
# part 1
id_list_go <- enrichGO(gene = id_list_biomart$entrezgene_id, 'org.Hs.eg.db', pvalueCutoff = 0.05, pAdjustMethod = "BH", universe = names(background_biomart$entrezgene_id), minGSSize = 5, maxGSSize = 500, qvalueCutoff = 0.05, readable = TRUE)
head(id_list_go)
cnetplot(id_list_go)
upsetplot(id_list_go)
# part 2
id_list_mkegg <- enrichMKEGG(gene = id_list_biomart$entrezgene_id, pvalueCutoff = 0.1, pAdjustMethod = "BH", universe = names(background_biomart$entrezgene_id), minGSSize = 5, maxGSSize = 500, qvalueCutoff = 0.1)
head(id_list_mkegg)
cnetplot(id_list_mkegg)
upsetplot(id_list_mkegg)
# part 3
id_list_dgn <- enrichDGN(gene = id_list_biomart$entrezgene_id, pvalueCutoff = 0.05, pAdjustMethod = "BH", universe = names(background_biomart$entrezgene_id), minGSSize = 5, maxGSSize = 500, qvalueCutoff = 0.05, readable = TRUE)
head(id_list_dgn)
cnetplot(id_list_dgn)
upsetplot(id_list_dgn)
# GO without background
id_list_go_noBckg <- enrichGO(gene = id_list_biomart$entrezgene_id, 'org.Hs.eg.db', pvalueCutoff = 0.05, pAdjustMethod = "BH", minGSSize = 5, maxGSSize = 500, qvalueCutoff = 0.05, readable = TRUE)
head(id_list_go_noBckg)
cnetplot(id_list_go_noBckg)
upsetplot(id_list_go_noBckg)
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