Mining Process Function Links: Difference between revisions

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== Using existing annotations ==


#process_function_prob  process function        genesInBoth    genesWithFunc  genesWithProc  probProcessGivenFunction        probFunctionGivenProcess
[[Mining_Process_Function_Links_from_Annotations]]


The list shows various P and F pairs, and for each pair calculates statistics:
Drawbacks:


genesWithFunc = total genes annotated to F
* incomplete annotations
genesWithProc = total genes annotated to P
* annotation bias


(IEAs excluded)
== Using Pathway Databases ==


genesInBoth = total genes annotated to BOTH P and F.
[[Mining_Process_Function_Links_from_Reactome]]


probProcessGivenFunction = p(P | F)
== Using Obol ==
probFunctionGivenProcess = p(F | P)


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
[[XP:biological_process_xp_molecular_function]]


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
[[Category:Ontology]]
 
[[Category:Function-Process]]
{|class="wikitable" style="text-align:center"
[[Category:Electron transport]]
|+ Process Function Links
|-
| 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
|}

Latest revision as of 19:11, 24 March 2009

Using existing annotations

Mining_Process_Function_Links_from_Annotations

Drawbacks:

  • incomplete annotations
  • annotation bias

Using Pathway Databases

Mining_Process_Function_Links_from_Reactome

Using Obol

XP:biological_process_xp_molecular_function