Can't Make Sense Of Gene Symbols

Question

[sinifdosyalari12h]

Sorry in advance if I am doing something completely meaningless as I am very new to gene ontology and bioinformatics.

I am using gene ontology for a small learning project and my ultimate goal is obtaining a list of entrez gene ids. However it is not possible to obtain entrez ids from the database so I have to work with gene symbols.

I am using the mygene python library to get the entrez id of some symbols.Using the mygene library I can check the symbols and aliases and get entrez ids. However I can't convert every gene symbol to an entrez id this way. Even when I try to set the scope and field to "all" there are symbols which return no hits.

Any suggestions on converting gene symbols to entrez ids is appreciated.

Or if anybody could help me make sense of these gene symbols I would be thankful(I tried googling some but some returned nothing while lead me to deeper confusion):

A2RUA4
A6ND21
A6NDM0
A6NDV5
A6NDX5
A6NE68
A6NEC0
A6NF35
A6NFC0
A6NFE1
A6NFK1
A6NFR3
A6NG73
A6NGH9
A6NGZ2
A6NH08
A6NHQ2
A6NJ58
A6NJ64
A6NJ87
A6NJD2
A6NK05
A6NK21
A6NK31
A6NK39
A6NKB0
A6NKX1
A6NLC8
A6NMX9
A6XGL8
A6XGM2
A6XGM3
A6XGM6
A6XGM8
A7LQ08
A8K014
A8K1J1
A8K3J7
A8K3M1
A8K3P5
A8K4M4
A8K549
A8K557
A8K581
A8K5A9
A8K5K4
A8K5N8
A8K607
A8K6A1
A8K6R9
A8K6Z7
A8K6Z9
A8K7L7
A8KAG7
A8MPP1
A8MS99
A8MSY0
A8MT22
A8MT96
A8MTE8
A8MTY0
A8MU69
A8MUF5
A8MUP4
A8MVD6
A8MVP4
A8MVW9
A8MVY7
A8MW26
A8MW45
A8MWD9
A8MXS6
A8MXV9
A8MYF4
A8MYH7
A8MYJ9
A8MYM2
A8MYN1
A8MYQ5
A8MZ49
A8MZF2
A8WDG6
A9LSF3
A9UK02
A9UL17
AVGR5
AVGR8
B2R768
B2R9H1
B3KM92
B3KNQ9
B3KNT8
B3KPC8
B3KPI7
B3KQ05
B3KQ61
B3KQP7
B3KR99
B3KRG6
B3KRR0
B3KSX8
B3KSZ2
B3KT27
B3KT62
B3KTH8
B3KUX4
B3KV47
B3KVB9
B3KWP0
B3KXF6
B3KXL9
B3KY84
B3KY92
CGI-117
CYCT1b
DKFZp313E1411
DKFZp434G222
DKFZp434K202
DKFZp434L0650
DKFZp434N1212
DKFZp547B0614
DKFZp571N1833
DKFZp572F2170
DKFZp586K2222
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DKFZp686A11192
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FLJ00110
FLJ00320
FLJ00380
GIOT3
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HOX2.8
HP8
HPX-42
HPX-5
HSPC114
HZF14
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KIAA0543
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LOC728395
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MSL1L1
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NP_003299
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OTTHUMP00000177641
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OTTHUMP00000178325
OTTHUMP00000178342
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P0C6E5
P61571
P61572
P61574
P61575
P61576
P61578
P61580
P61581
P61582
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Q05D88
Q05DF4
Q06DQ3
Q07644
Q12771
Q12998
Q13060
Q13537
Q13771
Q14546
Q14547
Q15288
Q15625
Q15636
Q15736
Q15918
Q16247
Q16365
Q16464
Q16466
Q16624
Q2VXS7
Q2VXS8
Q4U0F0
Q504R3
Q53EW1
Q53FZ4
Q53GX1
Q53XZ7
Q53YE0
Q59EB5
Q59EG4
Q59EI0
Q59EI6
Q59EI7
Q59EL8
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Q59F07
Q59F14
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Q59FT1
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Q59FW1
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Q6YL39
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Q6ZNF9
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[GenoMax]

Many of these may be obsolete records that no longer exist. These things happen as new genome builds come out. Examples:
https://www.uniprot.org/uniprot/Q6ZW69
https://www.ncbi.nlm.nih.gov/protein/XP_497547.3?report=genpept

[sinifdosyalari12h]

Thank you for the reply. The gene symbols being obsolete makes sense. So I went back to gene ontology and tried to see if I can get the obsolete genes from there to see if it would return a similar result to mine, however my sql query for obsolete human genes only returns around 20 genes.So is gene ontology not up to date or is there another problem

my sql code is:

SELECT
 is_obsolete,
 gene_product.symbol AS gp_symbol,
 gene_product.symbol AS gp_full_name,
 dbxref.xref_dbname AS gp_dbname,
 dbxref.xref_key AS gp_acc,
 db.fullname
FROM term
 INNER JOIN association ON term.id=association.term_id)
 INNER JOIN gene_product ON (association.gene_product_id=gene_product.id)
 INNER JOIN species ON (gene_product.species_id=species.id)
 INNER JOIN dbxref ON (gene_product.dbxref_id=dbxref.id)
 INNER JOIN db ON (association.source_db_id=db.id)
WHERE
 species.ncbi_taxa_id = '9606'
AND 
is_obsolete='1';

[GenoMax]

You can't query a current copy of the database (I assume that is what you did) and expect to find these. As genome builds get refined some gene predictions no longer make sense, there is no experimental evidence for some and some may just be identified as plain errors. As far as current versions of the database are concerned many of these are no longer real. If you look at the historic record for this entry you can see that it was always a computer prediction (no experimental evidence) and it was eventually dropped from the database.

What exactly are you trying to do?

[sinifdosyalari12h]

Oh so if I understand correctly the latest version of the Gene Ontology will not have many obsolete genes because if the latest version contained these obsolete genes then these genes would not really be obsolete.

What exactly are you trying to do?

Well my main goal is getting the genes(in Entrez ID form) related to certain GO terms. These GO terms are defined by the user.The user also specifies the ncbi taxonomy id so that I get the genes related to that species. To do this automatically, I connect to the

ensembldb.ensembl.org

SQL server and use ensembl_go_54 database. I do this via a python code. I then execute an SQL query on this database to get the genes annotated to the given GO term and species. From this query I am able to obtain gene symbols and I am unable to convert some of these symbols to entrez gene ids.

Initially I thought using an online mirror would be faster compared to setting up a local one. But now I suspect that the GO mirror that I am using is an older version and it gives me some obsolete gene symbols. I will now try setting up a local go database to see if that leads to anything different. I will update this comment after I try that. Thanks

[GenoMax]

This is a rather unusual use case (normally people want to go from genes to GO). Have you looked at http://geneontology.org/ and the downloads they provide?

[sinifdosyalari12h]

This is a rather unusual use case (normally people want to go from genes to GO)

I agree while I was googling about my problem I found many more posts related to that problem.

Have you looked at http://geneontology.org/ and the downloads they provide?

Yes I did but couldn't see something that would help me.

My current situation:I set up a local gene ontology database on my computer using the sql files they provide. I ran a test case on the database and obtained the gene symbols. Now I will see if I can convert these gene symbols, will keep you updated.

[sinifdosyalari12h]

Update: The local server gave almost twice as much gene symbols compared to my other solutions. With this set of gene symbols I did 2 things.

• I tried converting these symbols using the mygene python library. Which was able to give around 5k unique ids.

• I parsed the gene2accesion file(8 GB file provided by ncbi) to get entrez ids of these gene symbols. This also returned around 5k unique entrez ids.

  When I compared the two sets I saw that they shared around 4900 ids and there were 120 gene ids which weren't mutual. I will investigate this difference further but I think it is an acceptable error margin.
  I will also look into the thousands of gene symbols which weren't converted to anything, I am guessing they are proteins etc. and not really genes.

[GenoMax]

I am guessing they are proteins etc. and not really genes.

Minimally there is one gene = one protein (for genes that code for proteins, then there are isoforms, which are variants produced from same gene). What remains in your list is probably all defunct entries that you will have to ignore.

gene2accession file is the most current state of things. It gets generated every day.

[sinifdosyalari12h]

I also stumbled across gene2go provided by ncbi. It seems useful too, do you know how frequently updated that file is

[GenoMax]

All gene2* files are updated nightly everyday.

[sinifdosyalari12h]

Ok thank you.

If the gene2go file is complete-and it seems like that- that might be the answer for me. It is updated nightly as you say so I don't have to worry about getting obsolete results. It is also a small file (145 mb) so it is easy to download and easy to parse.

Compared to my other solution which is to download an 8 gb(gene2accesion) file and also download and setup the gene ontology sql database on my computer, downloading a 145 mb file is much more logical.

My main goal was to get the genes related to GO ID's and it seems like the gene2go file has that information along with species and evidence information. If gene2go is a complete file that contains all the gene-go relations I think I will continue with that, if you have any remarks feel free to tell me.

Thank you very much for caring and responding to my questions.

[jared.andrews07]

Yeah, I would personally not bother with them given that they won't come up in any other annotations really. On an unrelated note, submitting multiple questions for the same issue is unlikely to get you any further help. Try to limit yourself to a single question for a given issue. It makes it easier to track for those of us interested in helping.

[sinifdosyalari12h]

Thank you for the suggestion. As you can probably tell I am a beginner to all these stuff so I thought if I phrased myself and my problem differently somebody would be able to help me.

[jared.andrews07]

It's okay. People here are pretty stubborn - if you pose an interesting, well-written question with proper background, they'll usually do their best to help once they get invested. It might take some time (a few days between comments/answers even), but we generally want to help you find the answer and learn as well. Biostars is odd in that it has a lot of users, but it's still a rather small community - you will grow to recognize/remember the most active members pretty quickly.