Question: Which Conversion tool is more good?
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gravatar for aouichechaimaa
18 months ago by
aouichechaimaa130 wrote:

Hi, guys, I got HumanNet data which have GeneIDs and I want to get the gene names of these IDs This data have interactions between 2 GeneIDs but i want the gene names of these interactions I have tried two tools UnitProtKB and bioDBnet. By using UnitProtKB i found some rows have multiple gene names with multiple IDs and i can't understand which gene i will take for which identifier or i have to delete this rows or re-annotate it again or what???? Here is a link to some rows from the file i got.

![enter image description here][1] [1]: https://ibb.co/fso2Vk

ADD COMMENTlink modified 18 months ago by Devon Ryan86k • written 18 months ago by aouichechaimaa130

Could anyone explain to me this issue or suggest me to up-to date tools beside the tools i used ?

ADD REPLYlink written 18 months ago by aouichechaimaa130
0
gravatar for Devon Ryan
18 months ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

Google a few of those, you'll see you're noticing (at least mostly) genes with multiple names.

ADD COMMENTlink written 18 months ago by Devon Ryan86k

@Devon Ryan what do you mean? which gene name i will take? the text file is very huge, do i need to google all of them???

ADD REPLYlink written 18 months ago by aouichechaimaa130

What do you think?

ADD REPLYlink written 18 months ago by Devon Ryan86k

it's impossible and that's my question how to deal with this data to get the right match names say: P49736 MCM2 BM28 CCNL1 CDCL1 KIAA0030 4171; In this row geneID 4171 is corresponding only to MCM2 what about the other genes? plz Any help i appreciate it !

ADD REPLYlink written 18 months ago by aouichechaimaa130
1

You seem to be vastly over thinking this. The first name listed is the official name, the others are alternatives. Just take the first name and be done with it.

ADD REPLYlink written 18 months ago by Devon Ryan86k

@ Devon Ryan Thanks a lot, Friend .

Another case: P62807 HIST1H2BC H2BFL; HIST1H2BE H2BFH; HIST1H2BF H2BFG; HIST1H2BG H2BFA; HIST1H2BI H2BFK 8339,3017,8343,8347,8346,8344. In this case, there are 10 genes and the first five genes are official names as you say, but there are 6 IDs and so, do I have to delete the ID which not corresponds to any gene is it right?

I can't understand why UnitProt is giving annotation like this despite I selected Filter by reviewed SwissProt?

According to your experience, Could you suggest me to any conversion tool that can give good annotation or which tool are you considering in your daily research?

Sorry if I bother you by asking a multitude of questions

ADD REPLYlink written 18 months ago by aouichechaimaa130
1

That appears to be a case of multiple genes producing the exact same thing. Again, just take the first one.

ADD REPLYlink written 18 months ago by Devon Ryan86k

means the 6th ID will be deleted right? and what about the good conversion tool?

ADD REPLYlink written 18 months ago by aouichechaimaa130

means the 6th ID will be deleted right?

That means all but the first will be deleted.

and what about the good conversion tool?

There is only one mapping between the ids, the results should be the same regardless of what you use.

ADD REPLYlink written 18 months ago by Devon Ryan86k

@ Devon Ryan friend; I mean when i checked the mapping 3017 id doesn't match any gene and i have to delete it .

ADD REPLYlink written 18 months ago by aouichechaimaa130
1

Then no known gene produces those proteins. All tools and sites use the same conversion list.

ADD REPLYlink written 18 months ago by Devon Ryan86k
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