Mining Process Function Links from Annotations

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We can mine potential PF links using existing annotations. If two terms are frequently co-annotated there is a likely relationship between them, and there is an argument for representing this in the ontology.

PF annots table

The column headings (line 1) are:

  1. process
  2. function
  3. genesInBoth : total genes annotated to BOTH P and F.
  4. genesWithFunc  : total genes annotated to F
  5. genesWithProc  : total genes annotated to P
  6. probProcessGivenFunction  : p(P | F)
  7. probFunctionGivenProcess  : p(F | P)

(IEAs excluded)

Note that for all calculations, logically entailed annotations are used, not asserted annotations. A gene G is considered to be annotated to X if it is directly annotated to X (asserted), or indirectly via the graph (logically entailed)

  • if p(P | F) is high and we have a statistically significant sample size, then there is support for a F part_of P link
  • if p(F | P) is high and we have a statistically significant sample size, then there is support for a P has_part F link

IMPORTANT NOTE: even if in biological reality a P has_part F exists, we do not expect to see p(F|P) ~= 1. This is because a process consists of many function executions; a gene G that is involved in P must have the function of executing *one* of the parts of P, but we can't say which one unless we have function evidence - see the has_part documentation for more. Contrast this with the opposing case: if a function F is always part_of a process P, then a gene whose function is to execute F necessarily is involved in P.

Results

Photosynthetic Electron Chain

Jen mentioned the idea of mining links from existing annotations, via Michelle. Specifically, the group working on electron transport (cc'd - not sure if they are already on the fp list) were interested in finding existing function annotations from annotations to photosynthetic electron transport chain and photosynthetic light reaction. Amigo queries were too repetitive.

Results are available in: go/scratch/fp-links/pfprobs-pschain.tbl

process function genesInBoth genesWithFunc genesWithProc probProcessGivenFunction probFunctionGivenProcess
GO:0009767-photosynthetic electron transport chain GO:0005375-copper ion transmembrane transporter activity 1 76 128 0.0132 0.0078
GO:0009767-photosynthetic electron transport chain GO:0005507-copper ion binding 1 293 128 0.0034 0.0078
GO:0009767-photosynthetic electron transport chain GO:0015662-ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism 1 350 128 0.0029 0.0078
GO:0009772-photosynthetic electron transport in photosystem II GO:0003959-NADPH dehydrogenase activity 1 22 4 0.0455 0.2500
GO:0009772-photosynthetic electron transport in photosystem II GO:0045157-electron transporter, transferring electrons within the noncyclic electron transport pathway of photosynthesis activity 1 2 4 0.5000 0.2500
GO:0009772-photosynthetic electron transport in photosystem II GO:0046428-1,4-dihydroxy-2-naphthoate octaprenyltransferase activity 1 2 4 0.5000 0.2500
GO:0009773-photosynthetic electron transport in photosystem I GO:0003677-DNA binding 1 9893 7 0.0001 0.1429
GO:0009773-photosynthetic electron transport in photosystem I GO:0005516-calmodulin binding 1 373 7 0.0027 0.1429
GO:0009773-photosynthetic electron transport in photosystem I GO:0009055-electron carrier activity 1 1152 7 0.0009 0.1429
GO:0009775-photosynthetic electron transport in cytochrome b6/f GO:0045158-electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity 2 2 5 1.0000 0.4000
GO:0009775-photosynthetic electron transport in cytochrome b6/f GO:0046028-electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity 1 1 5 1.0000 0.2000
GO:0010205-photoinhibition GO:0004176-ATP-dependent peptidase activity 1 56 7 0.0179 0.1429
GO:0010205-photoinhibition GO:0004722-protein serine/threonine phosphatase activity 1 417 7 0.0024 0.1429
GO:0010205-photoinhibition GO:0005198-structural molecule activity 1 4123 7 0.0002 0.1429
GO:0010205-photoinhibition GO:0008237-metallopeptidase activity 1 481 7 0.0021 0.1429
GO:0010205-photoinhibition GO:0008266-poly(U) binding 2 33 7 0.0606 0.2857
GO:0010205-photoinhibition GO:0008270-zinc ion binding 1 1396 7 0.0007 0.1429
GO:0010205-photoinhibition GO:0009979-16:0 monogalactosyldiacylglycerol desaturase activity 1 1 7 1.0000 0.1429
GO:0010205-photoinhibition GO:0010242-oxygen evolving activity 2 2 7 1.0000 0.2857
GO:0010205-photoinhibition GO:0016887-ATPase activity 1 4197 7 0.0002 0.1429
GO:0010205-photoinhibition GO:0045485-omega-6 fatty acid desaturase activity 1 2 7 0.5000 0.1429
GO:0019684-photosynthesis, light reaction GO:0008266-poly(U) binding 3 33 262 0.0909 0.0115
GO:0019684-photosynthesis, light reaction GO:0008839-dihydrodipicolinate reductase activity 1 22 262 0.0455 0.0038
GO:0019684-photosynthesis, light reaction GO:0010242-oxygen evolving activity 2 2 262 1.0000 0.0076
GO:0019684-photosynthesis, light reaction GO:0016168-chlorophyll binding 11 33 262 0.3333 0.0420
GO:0019684-photosynthesis, light reaction GO:0020037-heme binding 2 208 262 0.0096 0.0076
GO:0019684-photosynthesis, light reaction GO:0030385-ferredoxin:thioredoxin reductase activity 2 4 262 0.5000 0.0076

AmiGO query: all annotations for photosynthetic electron transport chain genes