Question: Finding Gene Name Synonyms
1
gravatar for Ark
13 months ago by
Ark70
US
Ark70 wrote:

Hello again,

I was curious if anyone had a nice way of finding the gene synonyms for a list of genes? My genes are currently listed as gene symbols, however, any tool or method to fetch synonyms from any type of ID would be a step in the right direction. Conversions in the reverse direction would also be helpful (from any known synonym to gene symbol).

As an example: If I came across IL8 (a synonym), I would convert it to CXCL8 (the gene symbol), or vice-versa. I know in ENSEMBL (and many other tools) you can search for genes using many synonymous names, so there must be a table somewhere to easily covert between the two, but I have not been able to locate it.

Currently, I am using a massive table from UniProt and using 'awk' to search for the genes I need. This is both cumbersome and inefficient, which is why I wanted to reach out to you all!

Thanks!

R gene • 667 views
ADD COMMENTlink modified 13 months ago by cmdcolin1.3k • written 13 months ago by Ark70
5
gravatar for Pierre Lindenbaum
13 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

using mysql / ucsc

~$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 -D hg38 -e 'select distinct K2.alias from kgAlias as K1, kgAlias as K2 where K1.alias="IL8" and K1.kgID=K2.kgID;'
+-------------------+
| alias             |
+-------------------+
| B2R4L8            |
| CXCL8             |
| ENST00000307407.7 |
| IL8               |
| IL8_HUMAN         |
| NM_000584         |
| P10145            |
| Q6FGF6            |
| Q6LAE6            |
| Q96RG6            |
| Q9C077            |
| Q9UCE1            |
| Q9UCR8            |
| Q9UCR9            |
| Q9UCS0            |
| uc003hhe.1        |
| uc003hhe.2        |
| uc003hhe.3        |
| C9J4T6            |
| C9J4T6_HUMAN      |
| ENST00000401931.1 |
| LP896310          |
| uc062xgp.1        |
+-------------------+
ADD COMMENTlink written 13 months ago by Pierre Lindenbaum126k

Thank you very much Pierre! This was exactly what I was looking for!

ADD REPLYlink written 13 months ago by Ark70
2
gravatar for cmdcolin
13 months ago by
cmdcolin1.3k
United States
cmdcolin1.3k wrote:

You might also consider mygene.info

curl "http://mygene.info/v3/query?q=CXCL8&species=human&fields=all"

If you have jq, you can sort of slice and dice the results. This chooses the top hit (make sure to validate this in whatever case you are in) and picks fields from it

Pick some aliases

curl "http://mygene.info/v3/query?q=CXCL8&species=human&fields=all"|jq ".hits[0].alias"
[
  "GCP-1",
  "GCP1",
  "IL8",
  "LECT",
  "LUCT",
  "LYNAP",
  "MDNCF",
  "MONAP",
  "NAF",
  "NAP-1",
  "NAP1"
]

Pick some ensembl info

curl "http://mygene.info/v3/query?q=CXCL8&species=human&fields=all"|jq ".hits[0].ensembl"
{
  "gene": "ENSG00000169429",
  "protein": [
    "ENSP00000306512",
    "ENSP00000385908"
  ],
  "transcript": [
    "ENST00000307407",
    "ENST00000401931",
    "ENST00000483500"
  ],
  "translation": [
    {
      "protein": "ENSP00000306512",
      "rna": "ENST00000307407"
    },
    {
      "protein": "ENSP00000385908",
      "rna": "ENST00000401931"
    }
  ],
  "type_of_gene": "protein_coding"
}

Pick some crazy accessions

curl "http://mygene.info/v3/query?q=CXCL8&species=human&fields=all"|jq ".hits[0].accession"
{
  "genomic": [
    "AC112518.1",
    "AF385628.2",
    "CH471057.1",
    "D14283.1",
    "HC462818.1",
    "HI519526.1",
    "M28130.1",
    "NC_000004.12",
    "NG_029889.1"
  ],
  "protein": [
    "AAA35611.1",
    "AAA36323.1",
    "AAA59158.1",
    "AAH13615.1",
    "AAK60276.1",
    "AAP35730.1",
    "BAA03245.1",
    "BAG34815.1",
    "CAA68742.1",
    "CAA77745.1",
    "CAG46948.1",
    "CBK51144.1",
    "CBX54344.1",
    "EAX05687.1",
    "EAX05688.1",
    "EAX05689.1",
    "NP_000575.1",
    "NP_001341769.1",
    "P10145.1"
  ],
  "rna": [
    "AJ227913.1",
    "AK131067.1",
    "AK311874.1",
    "BC013615.1",
    "BG497712.1",
    "BT007067.1",
    "CR542151.1",
    "DA671239.1",
    "M17017.1",
    "M26383.1",
    "NM_000584.4",
    "NM_001354840.1",
    "Y00787.1",
    "Z11686.1"
  ],
  "translation": [
    {
      "protein": "BAG34815.1",
      "rna": "AK311874.1"
    },
    {
      "protein": "AAA35611.1",
      "rna": "M17017.1"
    },
    {
      "protein": "NP_000575.1",
      "rna": "NM_000584.4"
    },
    {
      "protein": "CAA68742.1",
      "rna": "Y00787.1"
    },
    {
      "protein": "CAA77745.1",
      "rna": "Z11686.1"
    },
    {
      "protein": "NP_001341769.1",
      "rna": "NM_001354840.1"
    },
    {
      "protein": "AAA36323.1",
      "rna": "M26383.1"
    },
    {
      "protein": "AAH13615.1",
      "rna": "BC013615.1"
    },
    {
      "protein": "CAG46948.1",
      "rna": "CR542151.1"
    },
    {
      "protein": "AAP35730.1",
      "rna": "BT007067.1"
    }
  ]
}

Pick some uniprot info

curl "http://mygene.info/v3/query?q=symbol:CXCL8&species=human&fields=all"|jq ".hits[0].uniprot"

{
  "Swiss-Prot": "P10145",
  "TrEMBL": [
    "C9J4T6",
    "A0A024RDA5"
  ]
}
ADD COMMENTlink written 13 months ago by cmdcolin1.3k
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