Thread by @tangming2005

1/ You’re merging gene data across tools. Suddenly nothing matches.
ENSEMBL, ENTREZ, TP53, P53…
Why so many gene IDs?

2/
Gene ID chaos is real.
One gene, three names: ENSEMBL ID, ENTREZ ID, gene symbol.
Different formats, same biology—but not always.

3/
ENTREZ ID is a stable integer from NCBI.
Example: TP53 = 7157

4/
ENSEMBL ID is versioned and specific.
TP53 = ENSG00000141510
Used in Ensembl, Gencode, and many RNA-seq pipelines.

5/
Then you have gene symbols.
TP53 is the official name.
But some still write P53 (not wrong—just outdated).

6/
Here’s the problem:
One ENSEMBL ID can link to multiple symbols.
One symbol can map to many ENSEMBL IDs.
Now you’re stuck.

7/
Why so messy?
Gene annotations evolve.
A new transcript is discovered.
A gene gets renamed.
Science moves, but your data might not.

8/
How do you fix this?
Use biomaRt in R to map IDs reliably.
It pulls live data from Ensembl. Here’s a working example:

9/
library(biomaRt)
mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
getBM(attributes = c("ensembl_gene_id", "entrezgene_id", "external_gene_name"),
filters = "ensembl_gene_id",
values = "ENSG00000141510",
mart = mart)

Returns TP53, 7157, and ENSEMBL ID.

10/
Prefer the browser?
Use Ensembl BioMart: ensembl.org/biomart/martvi…
Or NCBI Gene: ncbi.nlm.nih.gov/gene
Paste your ID—get all the links.

11/
Still getting P53 instead of TP53?
That’s a gene symbol alias.
Fix it with the HGNChelper package in R.

12/
install.packages("HGNChelper")
library(HGNChelper)
checkGeneSymbols("P53")

It corrects aliases and returns TP53.

13/
Now let’s go across species.
You’re comparing human and mouse data.
Use babelgene to find orthologs.

14/
install.packages("babelgene")
library(babelgene)
orthologs("BRCA1", species = "mouse")

Returns mouse Brca1 with corresponding IDs.

15/
You can also convert ENTREZ IDs with org.Hs.eg.db:
library(org.Hs.eg.db)
mapIds(org.Hs.eg.db, keys = "1017", column = "SYMBOL",
keytype = "ENTREZID", multiVals = "first")

Maps 1017 to CDK2.

16/
Gene names are messy:
Synonyms (P53 = TP53)

Aliases

Orthologs

Outdated IDs
They break pipelines if unchecked.

17/
Key takeaways:
Gene IDs are not interchangeable

Use HGNChelper to fix aliases

Use biomaRt and babelgene to convert reliably

Always double-check across species

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