genes missing from a network derived from a list which should be present

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Issue #97 closed
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Hi,

I uploaded my list from the search box.

The list is SPCC23B6.03c, SPAC13C5.07, SPAC1556.01c, SPBC6B1.09, SPCC338.08, SPBC216.05, SPCC1259.13, SPAC664.07c, SPAC20G4.04c, SPAC1952.07, SPBC342.05, SPCC622.08c, SPAC19G12.06

However, nbs1 does not appear in the resulting network.

I know it should, because it is part of a tripartite complex with mre11 and rad50 see fig nbs1 which shows this int eh cell cycle regulation network

fig "starting network" is what I see from this list.

I don't know if any other genes are missing. My preferred behavior would be like STRING, where the genes which are in your list, but not in the network are shown as unconnected nodes. Otherwise, you need to check one by one which are missing which isn't practical for large lists.

Comments (4)

  1. Dan Bean

    The problem is that the interaction data has nbs1 as SPBC6B1.09c (which is also the name from the pombase page), but it's just SPBC6B1.09 in your list. If I add the "c" to the end then nbs1 does appear in the network. I'm not really familiar with pombe systematic names, is the c something we could just ignore?

  2. Valerie Wood

    That's odd, I thought I exported the systematic IDs from PomBase as a list. Some systematic IDs do have a c suffix which somehow got lost from my list, so esyN is correct.

    Sorry about that.

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