Mining Process Function Links: Difference between revisions

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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 ==
[[Mining_Process_Function_Links_from_Annotations]]
 
[[Mining_Process_Function_Links_from_Reactome]]
The column headings (line 1) are:
 
# process
# function       
# genesInBoth : total genes annotated to BOTH P and F.
# genesWithFunc  : total genes annotated to F
# genesWithProc  : total genes annotated to P
# probProcessGivenFunction  : p(P | F)   
# 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 <code> p(P | F)</code> is high and we have a statistically significant sample size, then there is support for a F [[part_of]] P link
 
* if <code>p(F | P)</code> 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 <code>p(F|P) ~= 1</code>. 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: [http://www.geneontology.org/scratch/fp-links/pfprobs-pschain.tbl go/scratch/fp-links/pfprobs-pschain.tbl]
 
{|class="wikitable" style="text-align:center" border="1"
|-
| 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:
[http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=UniProtKB:Q7TUF3&amp;gp=UniProtKB:Q7U4U6&amp;gp=UniProtKB:Q7NNA0&amp;gp=UniProtKB:P0A3X9&amp;gp=UniProtKB:Q7VC24&amp;gp=TAIR:locus:2119265&amp;gp=UniProtKB:Q8Z0D7&amp;gp=TAIR:gene:3715303&amp;gp=TAIR:locus:2206061&amp;gp=UniProtKB:Q8DKI2&amp;gp=UniProtKB:Q7V7R5&amp;gp=UniProtKB:P46445&amp;gp=UniProtKB:P27589&amp;gp=UniProtKB:P58558&amp;gp=UniProtKB:Q8DKN2&amp;gp=UniProtKB:Q7U6N5&amp;gp=UniProtKB:Q93RE3&amp;gp=UniProtKB:Q9X9S9&amp;gp=UniProtKB:P0A384&amp;gp=UniProtKB:Q7NJB3&amp;gp=UniProtKB:Q7U8A1&amp;gp=UniProtKB:P61048&amp;gp=UniProtKB:P74159&amp;gp=UniProtKB:Q7V6M3&amp;gp=UniProtKB:P73500&amp;gp=UniProtKB:Q7V129&amp;gp=UniProtKB:Q7V5B9&amp;gp=UniProtKB:P73496&amp;gp=UniProtKB:P74149&amp;gp=UniProtKB:P58246&amp;gp=UniProtKB:Q93SX1&amp;gp=UniProtKB:Q7VDK9&amp;gp=UniProtKB:Q7VDK8&amp;gp=UniProtKB:Q57038&amp;gp=UniProtKB:P27319&amp;gp=UniProtKB:P27197&amp;gp=UniProtKB:P42351&amp;gp=UniProtKB:Q7NF27&amp;gp=UniProtKB:Q7V2X6&amp;gp=UniProtKB:Q93SW9&amp;gp=UniProtKB:Q7VBF3&amp;gp=UniProtKB:Q9X9T1&amp;gp=UniProtKB:Q7V1W2&amp;gp=UniProtKB:Q7NJB4&amp;gp=UniProtKB:P0A3D9&amp;gp=UniProtKB:Q7U4U7&amp;gp=UniProtKB:Q55318&amp;gp=UniProtKB:Q9X9S8&amp;gp=UniProtKB:P26287&amp;gp=UniProtKB:Q7TUQ1&session_id=4590amigo1221771698&page_size=all all annotations for photosynthetic electron transport chain  genes]
 
[[Category:Ontology]]
[[Category:Function-Process]]
[[Category:Electron transport]]

Revision as of 16:30, 24 September 2008

Mining_Process_Function_Links_from_Annotations Mining_Process_Function_Links_from_Reactome

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