8
$\begingroup$

I need to download all uniprotIDs of a cancer pathway, say the AKT Signaling. It may be super easy, but I don't know which resource to look at since it is a new field.

How/where do I find these?

Improve this question
$\endgroup$
1
  • 1
    $\begingroup$ Welcome to Biology S.E.! If you have additional question regarding asking questions on this site, please visit The help center $\endgroup$
    – L.B.
    Commented Feb 4, 2015 at 2:25

2 Answers 2

Reset to default
4
$\begingroup$

I would do this through the Reactome database. Searching for "AKT Signalling" returns, among other things, an entry for PI3K/AKT Signaling in Cancer (Homo sapiens) (REACT_147723). Clicking on that link will take you to the pathway's page, and if you click on "Disease" (under "Locations in the PathwayBrowser"), you will be shown a link to the pathway browser page of that particular pathway.

Once there, click on the "Molecules" tab, select "Proteins" and you will get a list of the proteins involved in the pathway and their UniProt accessions. There, you can click on the "Download" link and retrieve this list:

MoleculeType    Identifier  MoleculeName    
Proteins    P31751  UniProt:P31751 AKT2 
Proteins    P31749  UniProt:P31749 AKT1 
Proteins    Q9Y243  UniProt:Q9Y243 AKT3 
Proteins    P16220  UniProt:P16220 CREB1    
Proteins    Q12778  UniProt:Q12778 FOXO1    
Proteins    P98177  UniProt:P98177-2 FOXO4  
Proteins    O43524  UniProt:O43524 FOXO3    
Proteins    P98177  UniProt:P98177-1 FOXO4  
Proteins    O15530  UniProt:O15530 PDPK1    
Proteins    Q92934  UniProt:Q92934 BAD  
Proteins    P46527  UniProt:P46527 CDKN1B   
Proteins    P38936  UniProt:P38936 CDKN1A   
Proteins    Q00987  UniProt:Q00987 MDM2 
Proteins    P60484  UniProt:P60484 PTEN 
Proteins    Q8WWG1  UniProt:Q8WWG1 NRG4 
Proteins    P10721  UniProt:P10721 KIT  
Proteins    Q9HCT0  UniProt:Q9HCT0 FGF22    
Proteins    P15498  UniProt:P15498 VAV1 
Proteins    P05230  UniProt:P05230 FGF1 
Proteins    Q15303  UniProt:Q15303-1 ERBB4  
Proteins    P08620  UniProt:P08620 FGF4 
Proteins    P42338  UniProt:P42338 PIK3CB   
Proteins    O14944  UniProt:O14944 EREG 
Proteins    O15520  UniProt:O15520 FGF10    
Proteins    P21802  UniProt:P21802-3 FGFR2  
Proteins    Q13480  UniProt:Q13480 GAB1 
Proteins    P55075  UniProt:P55075-1 FGF8   
Proteins    O00459  UniProt:O00459 PIK3R2   
Proteins    Q9UEF7  UniProt:Q9UEF7-1 KL 
Proteins    P09619  UniProt:P09619 PDGFRB   
Proteins    Q8WU20  UniProt:Q8WU20 FRS2 
Proteins    Q86Z14  UniProt:Q86Z14 KLB  
Proteins    O00329  UniProt:O00329 PIK3CD   
Proteins    P11487  UniProt:P11487 FGF3 
Proteins    Q9GZV9  UniProt:Q9GZV9 FGF23    
Proteins    P42336  UniProt:P42336 PIK3CA   
Proteins    P42081  UniProt:P42081 CD86 
Proteins    P35568  UniProt:P35568 IRS1 
Proteins    P04626  UniProt:P04626 ERBB2    
Proteins    Q02297  UniProt:Q02297 NRG1 
Proteins    P12034  UniProt:P12034-1 FGF5   
Proteins    P56975  UniProt:P56975 NRG3 
Proteins    Q9NP95  UniProt:Q9NP95 FGF20    
Proteins    Q02297  UniProt:Q02297-10 NRG1  
Proteins    P22607  UniProt:P22607-2 FGFR3  
Proteins    P21802  UniProt:P21802-1 FGFR2  
Proteins    Q15303  UniProt:Q15303-2 ERBB4  
Proteins    P62993  UniProt:P62993-1 GRB2   
Proteins    O60258  UniProt:O60258-1 FGF17  
Proteins    P11362  UniProt:P11362-1 FGFR1  
Proteins    P15391  UniProt:P15391 CD19 
Proteins    Q9Y4H2  UniProt:Q9Y4H2 IRS2 
Proteins    Q99075  UniProt:Q99075 HBEGF    
Proteins    P21583  UniProt:P21583-1 KITLG  
Proteins    P31371  UniProt:P31371 FGF9 
Proteins    P27986  UniProt:P27986 PIK3R1   
Proteins    P22455  UniProt:P22455 FGFR4    
Proteins    P04085  UniProt:P04085-2 PDGFA  
Proteins    P06241  UniProt:P06241 FYN  
Proteins    P01127  UniProt:P01127 PDGFB    
Proteins    P21802  UniProt:P21802-5 FGFR2  
Proteins    Q06124  UniProt:Q06124 PTPN11   
Proteins    P21781  UniProt:P21781 FGF7 
Proteins    O95750  UniProt:O95750 FGF19    
Proteins    P21860  UniProt:P21860-1 ERBB3  
Proteins    O14511  UniProt:O14511 NRG2 
Proteins    P01133  UniProt:P01133 EGF  
Proteins    O76093  UniProt:O76093 FGF18    
Proteins    P21802  UniProt:P21802-18 FGFR2 
Proteins    O43320  UniProt:O43320 FGF16    
Proteins    P04085  UniProt:P04085-1 PDGFA  
Proteins    P10767  UniProt:P10767 FGF6 
Proteins    P06239  UniProt:P06239 LCK  
Proteins    Q92569  UniProt:Q92569 PIK3R3   
Proteins    Q6PIZ9  UniProt:Q6PIZ9 TRAT1    
Proteins    Q9UEF7  UniProt:Q9UEF7-2 KL 
Proteins    P35070  UniProt:P35070 BTC  
Proteins    P16234  UniProt:P16234 PDGFRA   
Proteins    P33681  UniProt:P33681 CD80 
Proteins    P22607  UniProt:P22607-1 FGFR3  
Proteins    P09038  UniProt:P09038 FGF2 
Proteins    P10747  UniProt:P10747 CD28 
Proteins    P00533  UniProt:P00533 EGFR 
Proteins    P55211  UniProt:P55211 CASP9    
Proteins    P22736  UniProt:P22736 NR4A1    
Proteins    Q6ZVD8  UniProt:Q6ZVD8 PHLPP2   
Proteins    O60346  UniProt:O60346 PHLPP1   
Proteins    Q9UKV8  UniProt:Q9UKV8 AGO2 
Proteins    Q9HCE1  UniProt:Q9HCE1 MOV10    
Proteins    Q9UPQ9  UniProt:Q9UPQ9 TNRC6B   
Proteins    Q9HCJ0  UniProt:Q9HCJ0 TNRC6C   
Proteins    Q9UL18  UniProt:Q9UL18 AGO1 
Proteins    Q8NDV7  UniProt:Q8NDV7 TNRC6A   
Proteins    Q9H9G7  UniProt:Q9H9G7 AGO3 
Proteins    Q9HCK5  UniProt:Q9HCK5 AGO4 
Proteins    Q96RU7  UniProt:Q96RU7 TRIB3    
Proteins    Q5T1C6  UniProt:Q5T1C6 THEM4    
Proteins    Q96B36  UniProt:Q96B36 AKT1S1   
Proteins    P49841  UniProt:P49841 GSK3B    
Proteins    P49840  UniProt:P49840 GSK3A    
Proteins    O15111  UniProt:O15111 CHUK 
Proteins    Q9BPZ7  UniProt:Q9BPZ7 MAPKAP1  
Proteins    Q6R327  UniProt:Q6R327 RICTOR   
Proteins    Q9BVC4  UniProt:Q9BVC4 MLST8    
Proteins    P42345  UniProt:P42345 MTOR 
Proteins    Q9UBS0  UniProt:Q9UBS0 RPS6KB2  
Proteins    P49815  UniProt:P49815 TSC2
Improve this answer
$\endgroup$
2
  • $\begingroup$ Thanks, that's great! Next thing would be to download the full network -> who interacts with whom. That would be great! $\endgroup$
    – El Dude
    Commented Feb 4, 2015 at 19:23
  • $\begingroup$ Ok, it's the SBML format. Found it. $\endgroup$
    – El Dude
    Commented Feb 4, 2015 at 19:31
2
$\begingroup$

The European Bioinformatics Institute (EBI) has a tool called "Quick GO", which allows you to search the Gene Ontology (GO) database using specific pathways or terms.

In the "Annotation Download" section (http://www.ebi.ac.uk/QuickGO/GAnnotation) enter your search term (e.g. "AKT signalling") and "search". QuickGO will present you with the search results, which for this search include;

  • protein kinase B signaling
  • regulation of protein kinase B signaling
  • positive regulation of protein kinase B signaling
  • negative regulation of protein kinase B signaling
  • ...

Select a pathway by clicking the GO ID (e.g. "GO:0043491" for "protein kinase B signaling"). This takes you to the information pages for this pathway.

To download the UniProt information (amongst other things) navigate to the "Protein Annotation" table using the tabs. In the top right you are presented with a "Download" option for the whole table (for this pathway containing 1,337 proteins)!

Hope that helps.

Improve this answer
$\endgroup$
2
  • $\begingroup$ This will not give you the proteins in the pathway, you say yourself there are more than a thousand results! What you are seeing are the many, many proteins that are somehow involved in that biological process, including the various regulatory proteins. This is not the pathway itself which only has a bit over 200 proteins. Remember that GO terms are inherited so if a protein is annotated to a child term of GO:0043491 (e.g. GO:0051896, regulation of protein kinase B signaling) it will also be annotated to GO:0043491. $\endgroup$
    – terdon
    Commented Feb 4, 2015 at 13:35
  • $\begingroup$ @terdon good point about child terms being included as well in GO terms - I have voted up your answer as it seems more appropriate in this context! $\endgroup$
    – Luke
    Commented Feb 4, 2015 at 14:58

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .