Protein Binding clean up

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Phase I of Protein Binding Clean-up: Removing gene product-specific binding terms.

Reasoning for obsoletion

There are 927 child terms of protein binding. The 69 terms listed below identify GO terms that describe binding to a specific protein, not a group of similarly functionning proteins. It should therefore be possible from the GO term used in the annotation, to determine what identifier should be included in the 'with' field and for the annotation to instead apply a sufficiently-descriptive parent term.

Terms that have a relationship with a receptor activity have been excluded from the list below, as they are required for full description of a signalling pathway in GO.

Future requests for terms that describe a type of protein binding will be considered with regards to the above criteria.

Attention has been paid to ensure that when these terms are obsoleted, a parent term is available that can capture enough information on the protein group the interactor belongs to. If a suitable, information-rich protein binding parent is not available, one has been suggested.

This first set of obsoletion suggestions has targeted terms which have a low number of manual annotations, therefore it is not intended to be complete, and it is more than likely that further GO terms, matching the above requirements will be identified in future.

GO terms recommended for obsoletion

  • Terms are supplied with number of manual direct annotations and suggested replacement term


1 GO:0017033 DNA topoisomerase I binding Action needed: only parent is enzyme binding, create a new parent term 'DNA topoisomerase binding' to capture annotations where the interactor could be either topoisomerase I or II?

1 GO:0031006 filamin-A binding Use instead: GO:0031005 filamin binding

0 GO:0031007 filamin-B binding Use instead: GO:0031005 filamin binding

0 GO:0031008 filamin-C binding Use instead: GO:0031005 filamin binding

0 GO:0051416 myotilin binding Use instead: GO:0008092 cytoskeletal protein binding

2 GO:0051419 nebulin binding Use instead: GO:0008092 cytoskeletal protein binding

0 GO:0051420 nebulette binding Use instead: GO:0008092 cytoskeletal protein binding

3 GO:0051370 ZASP binding Use instead: GO:0008092 cytoskeletal protein binding

0 GO:0051411 ALP binding Use instead: GO:0008092 cytoskeletal protein binding

0 GO:0043411 myopalladin binding Use instead: GO:0008092 cytoskeletal protein binding

6 GO:0048186 inhibin beta-A binding Use instead: GO:0034711 inhibin binding

0 GO:0034712 inhibin alpha binding Use instead: GO:0034711 inhibin binding

11 GO:0048187 inhibin beta-B binding Use instead: GO:0034711 inhibin binding

9 GO:0048154 S100 beta binding Action needed: Create a term to describe S-100 protein binding, a family of low molecular weight protein found in vertebrates

2 GO:0002163 alpha-dystroglycan binding

3 GO:0002166 beta-dystroglycan binding

1 GO:0002162 dystroglycan binding Action Needed: Currently GO:0005515 is the parent for these two terms. Should we create dystrophin-associated glycoprotein binding term, as a child of glycoprotein binding, which could also include the sarcoglycan, syntrophin protein interactors?)


8 GO:0051577 MyoD binding Use instead: GO:0043426 MRF binding

0 GO:0051578 Mrf4 binding Use instead: GO:0043426 MRF binding

0 GO:0051576 Myf5 binding Use instead: GO:0043426 MRF binding

0 GO:0051579 myogenin binding Use instead: GO:0043426 MRF binding

3 GO:0048184 follistatin binding Action Needed: Only replacement parent is 'protein binding' However, shouldn't it be a child of glycoprotein binding? Is this information-rich enough, esp as v. Few annotations – one ISS, a NAS and IPI exist from AgBase and UniProtKB.

1 GO:0050430 syntaxin-6 binding Use instead: GO:0019905 syntaxin binding

2 GO:0030349 syntaxin-13 binding Use instead: GO:0019905 syntaxin binding

2 GO:0051535 syntaxin-5 binding Use instead: GO:0019905 syntaxin binding

4 GO:0030347 syntaxin-2 binding Use instead: GO:0019905 syntaxin binding

1 GO:0034989 GTP-Ral binding Use instead: GO:0017160 Ral GTPase binding

3 GO:0051372 nonmuscle alpha-actinin binding Use instead: GO:0042805 actinin binding


2 GO:0051406 beta-actinin binding Use instead: GO:0042805 actinin binding

3 GO:0048187 inhibin beta-B binding Use instead: GO:0034711 inhibin binding

1 GO:0016030 metarhodopsin binding Use instead:GO:0002046 opsin binding

5 GO:0034187 apolipoprotein E binding Use instead: GO:0034185 apolipoprotein binding

5 GO:0072568 protein kinase C delta binding Use instead: GO:0005080 protein kinase C binding

3 GO:0097024 protein kinase C alpha binding Use instead: GO:0005080 protein kinase C binding

0 GO:0072569 protein kinase C eta binding Use instead: GO:0005080 protein kinase C binding


1 GO:0051374 FATZ 1 binding Use instead: GO:0051373 FATZ binding

0 GO:0051375 FATZ 2 binding Use instead: GO:0051373 FATZ binding

0 GO:0051376 FATZ 3 binding Use instead: GO:0051373 FATZ binding

8 GO:0042808 neuronal Cdc2-like kinase binding Use instead: GO:0019901 protein kinase binding

11 GO:0048602 fibroblast growth factor 1 binding Use instead: GO:0017134 fibroblast growth factor binding

8 GO:0048603 fibroblast growth factor 2 binding Use instead: GO:0017134 fibroblast growth factor binding

4 GO:0048604 fibroblast growth factor 3 binding Use instead: GO:0017134 fibroblast growth factor binding

0 GO:0048605 fibroblast growth factor 4 binding Use instead: GO:0017134 fibroblast growth factor binding

0 GO:0048606 fibroblast growth factor 5 binding Use instead: GO:0017134 fibroblast growth factor binding

0 GO:0048607 fibroblast growth factor 6 binding Use instead: GO:0017134 fibroblast growth factor binding

9 GO:0031014 troponin T binding Action Needed: Create new parent grouping term: 'troponin binding' that would capture Troponin C/T/I binding?

12 GO:0030172 troponin C binding Action Needed: Create new parent grouping term: 'troponin binding' that would capture Troponin C/T/I binding?

13 GO:0031013 troponin I binding Action Needed: Create new parent grouping term: 'troponin binding' that would capture Troponin C/T/I binding?

2 GO:0043106 GTP cyclohydrolase I binding Action Needed: Current parent is 'enzyme binding'. Make a GTP cyclohydrolase binding parent term to reduce information loss?

4 GO:0032145 succinate-semialdehyde dehydrogenase binding Action Needed:Create a more granular term than current parent 'enzyme binding', such as aldehyde dehydrogenase binding?


0 GO:0043239 laminin-4 binding Use instead:GO:0043236 laminin binding

1 GO:0043238 laminin-2 binding Use instead:GO:0043236 laminin binding

4 GO:0048405 neurotrophin-4/5 binding Use instead: GO:0043121 neurotrophin binding

7 GO:0048404 neurotrophin-3 binding Use instead: GO:0043121 neurotrophin binding

0 GO:0051526 NFAT 1 binding Use instead: GO:0051525 NFAT protein binding

0 GO:0051527 NFAT 2 binding Use instead: GO:0051525 NFAT protein binding

0 GO:0051528 NFAT 3 binding Use instead: GO:0051525 NFAT protein binding

0 GO:0051529 NFAT 4 binding Use instead: GO:0051525 NFAT binding

0 GO:0051529 NFAT 5 binding Use instead: GO:0051525 NFAT protein binding

0 GO:0017170 KU70 binding ' ' 'Action Needed: Current parent is 'protein binding'. Make a parent term 'ATP-dependent DNA helicase subunit binding' ?

12 GO:0070215 MDM2 binding ' ' 'Action Needed: ' ' ' Current parent is 'protein binding'. Make parent term 'MDM binding'?

0 GO:0070216 MDM4 binding ' ' 'Action Needed: ' ' ' Current parent is 'protein binding'. Make parent term 'MDM binding'?

0 GO:0032191 acrosin heavy chain binding Use instead: acrosin binding

0 GO:0032192 acrosin light chain binding Use instead: acrosin binding

Annotations affected by proposed obsoletion

Manual annotations

139 UniProtKB 73 MGI 3 ASPGD 7 FlyBase 159 RGD 2 SGD 4 ZFIN 4 WB 31 BHF-UCL 4 dictyBase 3 HGNC 1 AgBase

Electronic annotations

750 IEA annotations from Ensembl Compara (due to propagation of manual annotations)

SQL for groups to find manual annotations affected

Paste the below query into AmiGO's GOOSE, using your group's name.

SELECT concat(dbxref.xref_dbname, ':', dbxref.xref_key) AS dbx, gene_product.symbol, term.name, term.acc, evidence.code, db.name AS assigned_by FROM association, evidence, term, gene_product, dbxref, db WHERE (association.id = evidence.association_id) AND (association.gene_product_id = gene_product.id) AND (association.term_id = term.id) AND (gene_product.dbxref_id = dbxref.id) AND (association.source_db_id=db.id) AND evidence.code != 'IEA' AND term.acc IN ('GO:0017033','GO:0031006','GO:0031007','GO:0031008','GO:0051416','GO:0051419','GO:0051420','GO:0051370','GO:0051411','GO:0051411','GO:0043411','GO:0048186','GO:0034712','GO:0048187','GO:0048154','GO:0002163','GO:0002166','GO:0002162','GO:0051577','GO:0051578','GO:0051576','GO:0051579','GO:0048184','GO:0050430','GO:0030349','GO:0051535','GO:0030347','GO:0034989','GO:0051372','GO:0051393','GO:0051406','GO:0048187','GO:0016030','GO:0034187','GO:0034186','GO:0072568','GO:0097024','GO:0072569','GO:0048273','GO:0051374','GO:0051375','GO:0051376','GO:0042808','GO:0048602','GO:0048603','GO:0048604','GO:0048605','GO:0048606','GO:0048607','GO:0031014','GO:0030172','GO:0031013','GO:0043106','GO:0032145','GO:0043237','GO:0043239','GO:0043238','GO:0048405','GO:0048404','GO:0051526','GO:0051527','GO:0051528','GO:0051529','GO:0051529','GO:0017170','GO:0070215','GO:0070216','GO:0032191','GO:0032192') AND db.name = 'YOUR_DATABASE_NAME'

SQL for groups to find full details of manual annotations affected

select concat(dbxref.xref_dbname, ':', dbxref.xref_key) as dbx, gene_product.symbol, term.name, term.acc, evidence.code, concat(ev_dbxref.xref_dbname, ':', ev_dbxref.xref_key) as ev_dbx, evidence.seq_acc as with_string, db.name as assigned_by from association join evidence on (evidence.association_id = association.id) join term on (term.id = association.term_id) join gene_product on (gene_product.id = association.gene_product_id) join dbxref on (dbxref.id = gene_product.dbxref_id) join dbxref as ev_dbxref on (ev_dbxref.id = evidence.dbxref_id) join db on (db.id= association.source_db_id) where evidence.code != 'IEA' and ev_dbxref.xref_dbname = 'PMID' and term.acc in ('GO:0017033','GO:0031006','GO:0031007','GO:0031008','GO:0051416','GO:0051419','GO:0051420','GO:0051370','GO:0051411','GO:0051411','GO:0043411','GO:0048186','GO:0034712','GO:0048187','GO:0048154','GO:0002163','GO:0002166','GO:0002162','GO:0051577','GO:0051578','GO:0051576','GO:0051579','GO:0048184','GO:0050430','GO:0030349','GO:0051535','GO:0030347','GO:0034989','GO:0051372','GO:0051393','GO:0051406','GO:0048187','GO:0016030','GO:0034187','GO:0034186','GO:0072568','GO:0097024','GO:0072569','GO:0048273','GO:0051374','GO:0051375','GO:0051376','GO:0042808','GO:0048602','GO:0048603','GO:0048604','GO:0048605','GO:0048606','GO:0048607','GO:0031014','GO:0030172','GO:0031013','GO:0043106','GO:0032145','GO:0043237','GO:0043239','GO:0043238','GO:0048405','GO:0048404','GO:0051526','GO:0051527','GO:0051528','GO:0051529','GO:0051529','GO:0017170','GO:0070215','GO:0070216','GO:0032191','GO:0032192') ;