Hi guys, I am very new on R.
I have 4 csv files with gene sets X1, X2, X3, X4 and their corresponding logFC for E coil K12 strain under different conditions. X1, X2, X3 and X4 are gene IDs.
May you please advise/provide me with codes I can to use to generate a concatenated vector of entrez gene id for these gene sets along with their corresponding cutoff logFC at +/-0.5 (for upregulated and down regulated genes).
The used example from manual is at this code: lapply(gcSample, head) is on this link below
I need help.
Thank you in advance
•
written
by
tpm •
1 answer
Great, so, you can just use the Escherichia coli K-12 org.db that is in Bioconductor:
library(org.EcK12.eg.db)
genes <- c('glnD','eutC','mscM','tatA','elaB','fliI','sapD','ppnP',
'ybhA','ilvE','tatE','oppC')
mapIds(org.EcK12.eg.db, keys = genes,
column = 'ENTREZID', keytype = 'SYMBOL')
glnD eutC mscM tatA elaB fliI sapD ppnP
"944863" "946925" "948676" "948321" "946751" "946457" "946203" "945048"
ybhA ilvE tatE oppC
"945372" "948278" "945228" "945810"
With the Entrez IDs mapped, we can look up other stuff (and you can use clusterProfiler):
genes_entrez <- mapIds(org.EcK12.eg.db, keys = genes,
column = 'ENTREZID', keytype = 'SYMBOL')
keytypes(org.EcK12.eg.db)
[1] "ACCNUM" "ALIAS" "ENTREZID" "ENZYME" "EVIDENCE"
[6] "EVIDENCEALL" "GENENAME" "GO" "GOALL" "ONTOLOGY"
[11] "ONTOLOGYALL" "PATH" "PMID" "REFSEQ" "SYMBOL"
annotTable <- select(org.EcK12.eg.db, keys = genes_entrez,
columns = c('ENTREZID', 'ALIAS', 'ENZYME', 'SYMBOL', 'GENENAME', 'PATH'))
head(annotTable)
ENTREZID ALIAS ENZYME SYMBOL
1 944863 ECK0165 2.7.7.59 glnD
2 944863 glnD5 2.7.7.59 glnD
3 944863 glnD 2.7.7.59 glnD
4 946925 ECK2435 4.3.1.7 eutC
5 946925 eutC 4.3.1.7 eutC
6 948676 ECK4155 <NA> mscM
GENENAME PATH
1 PII uridylyltransferase/uridylyl removing enzyme 02020
2 PII uridylyltransferase/uridylyl removing enzyme 02020
3 PII uridylyltransferase/uridylyl removing enzyme 02020
4 ethanolamine ammonia-lyase subunit beta 00564
5 ethanolamine ammonia-lyase subunit beta 00564
6 miniconductance mechanosensitive channel MscM <NA>
Kevin
Thanks this help me a lot but how about convert the entrez id back into gene symbol? I have read the documentation but the example that they show in there is not clear like this topic. Any suggestion? Thanks in advance.
genes_entrez <- mapIds(org.EcK12.eg.db, keys = genes,
column = 'SYMBOL', keytype = 'ENTREZID')
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Downregulated Genes with GFOLD
written by jth
Please provide some sample input data.
For each set (X1 to X4) is the gene and the corresponding logFC. For example, this is an example of my dataset if I take just a few samples from it:
X1
X2
X3
X4